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Sample records for twelve microsatellite loci

  1. Isolation and characterization of twelve microsatellite loci for the Japanese Devilray (Mobula japanica)

    NARCIS (Netherlands)

    Poortvliet, Marloes; Galvan-Magana, Felipe; Bernardi, Giacomo; Croll, Donald A.; Olsen, Jeanine L.

    2011-01-01

    Twelve polymorphic microsatellites loci were characterized for Mobula japanica (Japanese Devilray) using an enrichment protocol. All but two loci were in Hardy-Weinberg equilibrium with no evidence of linkage disequilibrium or null-alleles for a sample of 40 individuals from two populations. The num

  2. Isolation and characterization of microsatellite loci from the yellow-eyed penguin (Megadyptes antipodes).

    Science.gov (United States)

    Boessenkool, S; King, T M; Seddon, P J; Waters, J M

    2008-09-01

    Twelve microsatellite loci were isolated and characterized in the endangered yellow-eyed penguin (Megadyptes antipodes) using enriched genomic libraries. Polymorphic loci revealed two to eight alleles per locus and observed heterozygosity ranged from 0.21 to 0.77. These loci will be suitable for assessing current and historical patterns of genetic variability in yellow-eyed penguins.

  3. Microsatellite loci for genetic mapping in the turkey (Meleagris gallopavo).

    Science.gov (United States)

    Reed, K M; Chaves, L D; Hall, M K; Knutson, T P; Rowe, J A; Torgerson, A J

    2003-11-01

    New microsatellite loci for the turkey (Meleagris gallopavo) were developed from two small insert DNA libraries. Polymorphism at these new loci was examined in domestic birds and two resource populations designed for genetic linkage mapping. The majority of loci (152 of 168) was polymorphic in domestic turkeys and informative in two mapping resource populations and thus will be useful for genetic linkage mapping.

  4. Characterization of microsatellite loci for the littorine snail Bembicium vittatum.

    Science.gov (United States)

    Kennington, W J; Lukehurst, S S; Johnson, M S

    2008-11-01

    We describe the isolation and development of 17 polymorphic microsatellite loci for the intertidal snail Bembicium vittatum (Gastropoda: Littorinidae). The loci were tested in 46 individuals from a single population situated near the centre of the species distribution. No evidence of linkage disequilibrium was detected between any pair of loci. However, two loci showed significant departures from Hardy-Weinberg expectations. The number of alleles per locus ranged from two to 15. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

  5. Evidence for heterozygote instability in microsatellite loci in house wrens.

    Science.gov (United States)

    Masters, Brian S; Johnson, L Scott; Johnson, Bonnie G P; Brubaker, Jessica L; Sakaluk, Scott K; Thompson, Charles F

    2011-02-23

    Microsatellite loci have high mutation rates and high levels of allelic variation, but the factors influencing their mutation rate are not well understood. The proposal that heterozygosity may increase mutation rates has profound implications for understanding the evolution of microsatellite loci, but currently has limited empirical support. We examined 20 microsatellite mutations identified in an analysis of 12 260 meiotic events across three loci in two populations of a songbird, the house wren (Troglodytes aedon). We found that for an allele of a given length, mutation was significantly more likely when there was a relatively large difference in size between the allele and its homologue (i.e. a large 'allele span'). Our results support the proposal of heterozygote instability at microsatellite loci.

  6. CHARACTERIZATION OF MICROSATELLITE LOCI IN SCHOENOPLECTUS AMERICANUS (CYPERACEAE)

    Science.gov (United States)

    Schoenoplectus americanus is a model organism for studying ecological and ecosystem responses of salt marsh plant communities to global climate change. Here we characterize 16 microsatellite loci in S. americanus to facilitate studies on the genetic basis of phenotypic responses...

  7. Ancient conservation of trinucleotide microsatellite loci in polistine wasps

    DEFF Research Database (Denmark)

    Ezenwa, V O; Peters, J M; Zhu, Y

    1998-01-01

    Microsatellites have proven to be very useful genetic markers for studies of kinship, parentage, and gene mapping. If microsatellites are conserved among species, then those developed for one species can be used on related species, which would save the time and effort of developing new loci. We e...

  8. Polymorphic microsatellite loci from two enriched genomic libraries for the genetic analysis of the miiuy croaker, Miichthys miiuy (Sciaenidae).

    Science.gov (United States)

    Wang, R X; Xu, T J; Sun, Y N; He, G Y

    2010-05-18

    Twelve polymorphic microsatellites from the (AG)(13) and (CA)(13) enriched genomic libraries of Miichthys miiuy were isolated and characterized in a test population; the number of alleles ranged from two to nine. The observed and expected heterozygosities ranged from 0.1923 to 1.0000 and from 0.2633 to 0.8337, respectively. Three loci deviated from Hardy-Weinberg equilibrium, and linkage disequilibrium between five pairs of loci was significant. These polymorphic microsatellite loci can be used for genetic diversity analysis and molecular-assisted breeding of M. miiuy.

  9. Isolation and characterization of the bovine microsatellite loci.

    Science.gov (United States)

    Chung, H Y; Kim, T H; Choi, B H; Jang, G W; Lee, J W; Lee, K T; Ha, J M

    2006-12-01

    Microsatellite loci were isolated using five repetitive probes for Korean native cattle. Eleven microsatellite loci were developed based on a biotin hybrid capture method, and enrichment of the genomic libraries (AAAT, TG, AG, T, and TGC repeats) was performed using Sau3AI adapters. The isolated markers were tested in two half-sib Korean cattle families and four imported breeds (Angus, Limousine, Holstein, and Shorthorn). Nine informative microsatellite loci were observed, and two microsatellite loci were revealed as monomorphic in Korean cattle. In the imported breeds, however, all of the markers were informative. In total, 213 alleles were obtained at the 11 loci across five breeds, and the average number of alleles found per locus, considering all populations, was 4.26. Heterozygosity was 0.71 (expected) and 0.57 (observed). The range of the polymorphic information content for the markers in all cattle populations was 0.43-0.69. Eleven percent of genetic variation was attributed to differentiation between populations as determined by the mean F (ST) values. The remaining 89% corresponded to differences among individuals. The isolated markers may be used to identify and classify the local breeds on a molecular basis.

  10. Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species

    Science.gov (United States)

    Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in three other Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. Nineteen microsatellite primers were tes...

  11. Microsatellite loci for the invasive colonial hydrozoan Cordylophora caspia

    Science.gov (United States)

    Cordylophora caspia, a colonial hydrozoan native to the Ponto-Caspian region, has become a common invader of both fresh and brackish water ecosystems of North America and Europe. Here we describe 11 polymorphic microsatellite loci for this species. Preliminary analyses indicate ...

  12. Polymorphic microsatellite loci for the crimson snapper (Lutjanus erythropterus).

    Science.gov (United States)

    Liu, L; Lin, L; Li, C H; Xu, S N; Liu, Y; Zhou, Y B

    2014-07-24

    We isolated and characterized 22 polymorphic microsatellite loci in Lutjanus erythropterus using a (GT)13-enriched genomic library. We found between 2 and 8 alleles per locus, with a mean of 4.85. The observed and expected heterozygosities ranged from 0.065 to 0.867 and from 0.085 to 0.832, respectively, with means of 0.461 and 0.529, respectively. Allele frequencies in three loci were found to deviate from Hardy-Weinberg equilibrium. Evidence for null alleles was found for three loci. These markers will be useful for distinguishing released captive-bred L. erythropterus individuals from wild individuals.

  13. Novel Microsatellite Loci Variation and Population Genetics within Leafy Seadragons, Phycodurus eques

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    Shawn Larson

    2014-01-01

    Full Text Available Novel leafy seadragon (Phycodurus eques microsatellite loci were developed via standard cloning techniques and tested for use in population genetics studies. Six out of a total of twelve microsatellites tested were usable for population analysis. Seadragon samples from Western Australia (N = 6, Southern Australia (N = 11, and a captive group (N = 11 were analyzed. Here, we present leafy seadragon microsatellite primer sequences for all 12 loci and population genetics statistics for the six loci that amplified consistently and displayed adequate variability to estimate population parameters, such as diversity, population differences, and relatedness. Observed heterozygosities ranged from 0.225 to 0.926 and expected heterozygosities ranged from 0.278 to 0.650. Pairwise differences among populations (FST estimates from samples collected off the southern coast of Western and South Australia, and captive animals ranged from a low of 0.188 between Southern Australia and captive animals, to a high of 0.212 between Western Australia and captive animals. Statistical assignment analyses suggested between one and three populations. Percent first order relatives among individuals was high and ranged from 40 within Western Australia to 55 within captive animals. These loci were tested on other species including weedy seadragons (Phyllopteryx taeniolatus, as well as assorted seahorses (Hippocampus reidi, H. erectus and pipefish (Doryrhamphus dactyliophorus, D. pessuliferus, Corythoichthys intestinalis, Syngnathus leptorhynchus with no success.

  14. Development of eighteen microsatellite loci in walleye (Sander vitreus)

    Science.gov (United States)

    Coykendall, Dolly K.; Morrison, Cheryl L.; Stott, Wendylee; Springmann, Marcus J.

    2014-01-01

    A suite of tri- and tetra-nucleotide microsatellite loci were developed for walleye (Sander vitreus) from 454 pyrosequencing data. Eighteen of the 50 primer sets tested amplified consistently in 35 walleye from two lakes on Isle Royale, Lake Superior: Chickenbone Lake and Whittlesey Lake. The loci displayed moderate levels of allelic diversity (average 5.5 alleles/locus) and heterozygosity (average 35.8 %). Levels of genetic diversity were sufficient to produce unique multi-locus genotypes and detect phylogeographic structuring as individuals assigned back to their population of origin. Cross-species amplification within S. canadensis(sauger) was successful for 15 loci, and 11 loci were diagnostic to species. The loci characterized here will be useful for detecting fine-scale spatial structuring, resolving the taxonomic status of Sander species and sub-species, and detecting walleye/sauger hybrids.

  15. Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species 1

    OpenAIRE

    Colby Witherup; Diane Ragone; Tyr Wiesner-Hanks; Brian Irish; Brian Scheffler; Sheron Simpson; Francis Zee; M. Iqbal Zuberi; Zerega, Nyree J. C.

    2013-01-01

    Premise of the study: Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. Methods and Results: A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241), A. camansi (34), A. mariannensis (1...

  16. Microsatellite Loci in Two Epiphytic Lichens with Contrasting Dispersal Modes: Nephroma laevigatum and N. parile (Nephromataceae

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    Rocío Belinchón

    2014-11-01

    Full Text Available Premise of the study: Microsatellite markers were characterized for two epiphytic cyanolichens, Nephroma laevigatum and N. parile (Nephromataceae, and will be used to investigate population structure and estimate gene flow among populations of these two closely related species with contrasting dispersal modes. Methods and Results: Twelve and 14 microsatellite loci were characterized for N. laevigatum and N. parile, respectively. Allele number in N. laevigatum ranged from three to 13 per locus, while in N. parile there were from two to six alleles per locus. As expected, the sexually reproducing N. laevigatum had higher genetic diversity than the predominantly asexual N. parile. Conclusions: This new set of markers is suitable for studying population structure and providing insights into gene flow among populations and for understanding processes of diversification. Compared between the species, they will facilitate an understanding of the influence of contrasting reproductive strategies on population and community structure.

  17. Characterization of Microsatellite Loci in Castilleja sessiliflora and Transferability to 24 Castilleja Species (Orobanchaceae

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    Jeremie B. Fant

    2013-06-01

    Full Text Available Premise of the study: Microsatellite primers were developed in the hemiparasitic perennial forb Castilleja sessiliflora to investigate patterns of gene flow and genetic diversity within and among populations. Methods and Results: Twelve polymorphic loci were identified in C. sessiliflora and tested on three populations (32 individuals each sampled across the range of the species. The loci amplified di- and trinucleotide repeats with 3–14 alleles per locus. To assess cross-amplification, primer pairs were also tested on 24 additional Castilleja species that represent the morphological and geographic diversity of the genus. We provide reports of their effectiveness in all 25 taxa. Conclusions: These results indicate the utility of these primers in C. sessiliflora for future studies of genetic structure and gene flow, as well as their widespread applicability in other members of the diverse and complex genus Castilleja.

  18. Isolation of microsatellite loci in the pollinating fig wasp of Ficus hispida, Ceratosolen solmsi

    Institute of Scientific and Technical Information of China (English)

    Hao Yu; Tong-Xin Zhang; Hao-Yuan Hu; Li-Ming Niu; Hui Xiao; Yan-Zhou Zhang; Da-Wei Huang

    2008-01-01

    Microsatellite loci were isolated for Ceratosolen solmsi, pollinator of the dioecious Ficus hispida. We developed nine polymorphic microsatellite loci based on the method of polymerase chain reaction isolation of microsatellite arrays (PIMA). Enrichment of genomic libraries was performed by random amplified polymorphic DNA (RAPD). A subset of 38 positive clones was sequenced; 15 clones showed microsatellite loci. We tested 15 designed primer pairs and nine of them produced polymorphic amplification in 48 individual wasps collected from different fruits of the dioecious host fig Ficus hispida in China. Among the 48 individuals, 49 alleles were obtained at the nine loci. The observed heterozygosity ranged between 0.357 and 0.634.

  19. Nine microsatellite loci developed from the octocoral, Paragorgia arborea

    Science.gov (United States)

    Coykendall, Dolly K.; Morrison, Cheryl L.

    2015-01-01

    Paragorgia arborea, or bubblegum coral, occurs in continental slope habitats worldwide, which are increasingly threatened by human activities such as energy development and fisheries practices. From 101 putative loci screened, nine microsatellite markers were developed from samples taken from Baltimore canyon in the western North Atlantic Ocean. The number of alleles ranged from two to thirteen per locus and each displayed equilibrium. These nuclear resources will help further research on population connectivity in threatened coral species where mitochondrial markers are known to lack fine-scale genetic diversity.

  20. Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species.

    Science.gov (United States)

    Witherup, Colby; Ragone, Diane; Wiesner-Hanks, Tyr; Irish, Brian; Scheffler, Brian; Simpson, Sheron; Zee, Francis; Zuberi, M Iqbal; Zerega, Nyree J C

    2013-07-01

    Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. • A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241), A. camansi (34), A. mariannensis (15), and A. altilis × mariannensis (64) samples. Nine of those loci plus four additional loci were evaluated on A. heterophyllus (jackfruit, 426) samples. All loci are polymorphic for at least one species. The average number of alleles ranges from two to nine within taxa. • These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species. They will aid in cultivar identification and establishing germplasm conservation strategies for breadfruit and jackfruit.

  1. Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species1

    Science.gov (United States)

    Witherup, Colby; Ragone, Diane; Wiesner-Hanks, Tyr; Irish, Brian; Scheffler, Brian; Simpson, Sheron; Zee, Francis; Zuberi, M. Iqbal; Zerega, Nyree J. C.

    2013-01-01

    • Premise of the study: Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. • Methods and Results: A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241), A. camansi (34), A. mariannensis (15), and A. altilis × mariannensis (64) samples. Nine of those loci plus four additional loci were evaluated on A. heterophyllus (jackfruit, 426) samples. All loci are polymorphic for at least one species. The average number of alleles ranges from two to nine within taxa. • Conclusions: These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species. They will aid in cultivar identification and establishing germplasm conservation strategies for breadfruit and jackfruit. PMID:25202565

  2. Development of Microsatellite Loci in Artocarpus altilis (Moraceae and Cross-Amplification in Congeneric Species

    Directory of Open Access Journals (Sweden)

    Colby Witherup

    2013-07-01

    Full Text Available Premise of the study: Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. Methods and Results: A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241, A. camansi (34, A. mariannensis (15, and A. altilis × mariannensis (64 samples. Nine of those loci plus four additional loci were evaluated on A. heterophyllus (jackfruit, 426 samples. All loci are polymorphic for at least one species. The average number of alleles ranges from two to nine within taxa. Conclusions: These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species. They will aid in cultivar identification and establishing germplasm conservation strategies for breadfruit and jackfruit.

  3. High polymorphism at microsatellite loci in the Chinese donkey.

    Science.gov (United States)

    Zhang, R F; Xie, W M; Zhang, T; Lei, C Z

    2016-06-24

    To reveal the genetic diversity and phylogenetic relationships between Chinese donkey breeds, 415 individuals representing ten breeds were investigated using ten microsatellite markers. The observed number of alleles, mean effective number of alleles (NE), mean expected heterozygosity (HE), and polymorphic information content (PIC) of each breed and polymorphic locus were analyzed. The results showed that seven (HTG7, HTG10, AHT4, HTG6, HMS6, HMS3, and HMS7) of ten microsatellite loci were polymorphic. The mean PIC, HE, and NE of seven polymorphic loci for the ten donkey breeds were 0.7679, 0.8072, and 6.0275, respectively. These results suggest that domestic Chinese donkey breeds possess higher levels of genetic diversity and heterozygosity than foreign donkeys. A neighbor-joining tree based on Nei's standard genetic distance showed that there was close genetic distance among Xinjiang, Qingyang, Xiji, and Guanzhong donkey breeds. In addition, Mongolia and Dezhou donkey breeds were placed in the same category. The phylogenetic tree revealed that the genetic relationships between Chinese donkey breeds are consistent with their geographic distribution and breeding history.

  4. Evolution of Microsatellite Loci of Tropical and Temperate Anguilla Eels

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    Mei-Chen Tseng

    2012-04-01

    Full Text Available Anguilla eels are divided into temperate and tropical eels, based on their major distributions. The present study collected two temperate eels, Anguilla japonica and Anguilla anguilla, and two tropical eels, Anguilla marmorata and Anguilla bicolor pacifica, to examine two questions: do temperate and tropical Anguilla eels have different genetic polymorphic patterns?; and do temperate Anguilla japonica and Anguilla anguilla have a closer relationship to each other than to tropical eels? In total, 274 sequences were cloned and sequenced from six conserved microsatellite loci to examine polymorphic patterns of these four catadromous eels. Different mutational events, including substitutions, and repeat-unit deletions and insertions, appeared in major regions, while different point mutations were observed in flanking regions. The results implied that parallel patterns of microsatellite sequences occurred within both tropical and temperate freshwater eels. Consensus flanking sequences of six homologous loci from each of the four species were constructed. Genetic distances ranged from 0.044 (Anguilla bicolor pacifica vs. Anguilla marmorata to 0.061 (Anguilla marmorata vs. Anguilla anguilla. The tree topology suggests the hypothesis of Anguilla japonica and Anguilla anguilla being a sister group must be rejected.

  5. Genetic diversity of microsatellite loci in hierarchically structured populations.

    Science.gov (United States)

    Song, Seongho; Dey, Dipak K; Holsinger, Kent E

    2011-08-01

    Microsatellite loci are widely used for investigating patterns of genetic variation within and among populations. Those patterns are in turn determined by population sizes, migration rates, and mutation rates. We provide exact expressions for the first two moments of the allele frequency distribution in a stochastic model appropriate for studying microsatellite evolution with migration, mutation, and drift under the assumption that the range of allele sizes is bounded. Using these results, we study the behavior of several measures related to Wright's F(ST), including Slatkin's R(ST). Our analytical approximations for F(ST) and R(ST) show that familiar relationships between N(e)m and F(ST) or R(ST) hold when the migration and mutation rates are small. Using the exact expressions for F(ST) and R(ST), our numerical results show that, when the migration and mutation rates are large, these relationships no longer hold. Our numerical results also show that the diversity measures most closely related to F(ST) depend on mutation rates, mutational models (stepwise versus two-phase), migration rates, and population sizes. Surprisingly, R(ST) is relatively insensitive to the mutation rates and mutational models. The differing behaviors of R(ST) and F(ST) suggest that properties of the among-population distribution of allele frequencies may allow the roles of mutation and migration in producing patterns of diversity to be distinguished, a topic of continuing investigation.

  6. Optimizing selection of microsatellite loci from 454 pyrosequencing via post-sequencing bioinformatic analyses.

    Science.gov (United States)

    Fernandez-Silva, Iria; Toonen, Robert J

    2013-01-01

    The comparatively low cost of massive parallel sequencing technology, also known as next-generation sequencing (NGS), has transformed the isolation of microsatellite loci. The most common NGS approach consists of obtaining large amounts of sequence data from genomic DNA or enriched microsatellite libraries, which is then mined for the discovery of microsatellite repeats using bioinformatics analyses. Here, we describe a bioinformatics approach to isolate microsatellite loci, starting from the raw sequence data through a subset of microsatellite primer pairs. The primary difference to previously published approaches includes analyses to select the most accurate sequence data and to eliminate repetitive elements prior to the design of primers. These analyses aim to minimize the testing of primer pairs by identifying the most promising microsatellite loci.

  7. Novel Microsatellite Loci for Sebaea aurea (Gentianaceae and Cross-Amplification in Related Species

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    Jonathan Kissling

    2013-12-01

    Full Text Available Premise of the study: Microsatellite loci were developed in Sebaea aurea (Gentianaceae to investigate the functional role of diplostigmaty (i.e., the presence of additional stigmas along the style. Methods and Results: One hundred seventy-four and 180 microsatellite loci were isolated through 454 shotgun sequencing of genomic and microsatellite-enriched DNA libraries, respectively. Sixteen polymorphic microsatellite loci were characterized, and 12 of them were selected to genotype individuals from two populations. Microsatellite amplification was conducted in two multiplex groups, each containing six microsatellite loci. Cross-species amplification was tested in seven other species of Sebaea. The 12 novel microsatellite loci amplified only in the two most closely related species to S. aurea (i.e., S. ambigua and S. minutiflora and were also polymorphic in these two species. Conclusions: These results demonstrate the usefulness of this set of newly developed microsatellite loci to investigate the mating system and population genetic structure in S. aurea and related species.

  8. Development and characterization of twelve microsatellite markers for Porphyra linearis Greville.

    Science.gov (United States)

    Varela-Álvarez, Elena; Paulino, Cristina; Serrão, Ester A

    2017-02-01

    The genus Porphyra (and its sister genus Pyropia) contains important red algal species that are cultivated and/or harvested for human consumption, sustaining a billion-dollar aquaculture industry. A vast amount of research has been focused on species of this genus, including studies on genetics and genomics among other areas. Twelve novel microsatellite markers were developed here for Porphyra linearis. Markers were characterized using 32 individuals collected from four natural populations of P. linearis with total heterozygosity varying from 0.098 to 0.916. The number of alleles per locus ranged from 2 to 18. All markers showed cross amplification with Porphyra umbilicalis and/or Porphyra dioica. These polymorphic microsatellite markers are useful for investigating population genetic diversity and differentiation in P. linearis and may become useful for other genetic research on the reproductive biology of this important species.

  9. Isolation and characterization of microsatellite loci from the Arctic cisco (Coregonus autumnalis)

    Science.gov (United States)

    Ramey, A.; Graziano, S.L.; Nielsen, J.L.

    2008-01-01

    Eight polymorphic microsatellite loci were isolated and characterized for the Arctic cisco, Coregonus autumnalis. Loci were evaluated in 21 samples from the Colville River subsistence fishery. The number of alleles per locus ranged from two to 18. Observed heterozygosity of loci varied from 0.10 to 1.00, and expected heterozygosity ranged from 0.09 to 0.92. All eight microsatellite markers were in Hardy-Weinberg equilibrium. The loci presented here will be useful in describing population structure and exploring populations of origin for Arctic cisco. ?? 2007 Blackwell Publishing Ltd.

  10. PERMANENT GENETIC RESOURCES: Isolation and characterization of microsatellite loci from the Arctic cisco (Coregonus autumnalis).

    Science.gov (United States)

    Ramey, A; Graziano, S L; Nielsen, J L

    2008-03-01

    Eight polymorphic microsatellite loci were isolated and characterized for the Arctic cisco, Coregonus autumnalis. Loci were evaluated in 21 samples from the Colville River subsistence fishery. The number of alleles per locus ranged from two to 18. Observed heterozygosity of loci varied from 0.10 to 1.00, and expected heterozygosity ranged from 0.09 to 0.92. All eight microsatellite markers were in Hardy-Weinberg equilibrium. The loci presented here will be useful in describing population structure and exploring populations of origin for Arctic cisco.

  11. CHARACTERIZATION OF MICROSATELLITE LOCI IN THE WIDELY INTRODUCED ESTUARINE ANEMONE NEMATOSTELLA VECTENSIS

    Science.gov (United States)

    We characterized ten polymorphic microsatellite loci from Nematostella vectensis, a burrowing anemone recently introduced to estuaries along the Pacific coast of North America and the southeast coast of England. Preliminary results indicate high variability and significant depar...

  12. CHARACTERIZATION OF MICROSATELLITE LOCI IN THE EUROPEAN GREEN CRAB (CARCINUS MAENAS)

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    Carcinus maenas (Decapoda: Portunidae) has proven a highly successful invasive marine species whose potential economic and ecological impacts are of great concern worldwide. Here, we characterize fourteen polymorphic microsatellite loci in C. maenas and its sister species C. Ae...

  13. Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries

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    Rodrigues NB

    2002-01-01

    Full Text Available In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3% sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds. Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8% contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds. The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds. From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci.

  14. Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries.

    Science.gov (United States)

    Rodrigues, N B; Loverde, P T; Romanha, A J; Oliveira, G

    2002-01-01

    In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3%) sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds). Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8%) contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds). The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds). From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci.

  15. Characterization of microsatellite loci for the Australian sea urchin Heliocidaris erythrogramma.

    Science.gov (United States)

    Binks, Rachel M; Lukehurst, Sherralee S; García-González, Francisco; Evans, Jonathan P

    2009-07-01

    We report 16 polymorphic microsatellite loci from Heliocidaris erythrogramma, a common sea urchin endemic to temperate Australian waters. These microsatellites were tested in a minimum of 30 individuals, which yielded between five and 14 alleles per locus. Expected heterozygosity ranged from 0.52 to 0.92 with four loci deviating from Hardy-Weinberg expectations. These markers are expected to be useful for experimental studies involving paternity analysis and for quantifying population structure in H. erythrogramma across its geographic range.

  16. Bottlenecks, population differentiation and apparent selection at microsatellite loci in Australian Drosophila buzzatii

    DEFF Research Database (Denmark)

    Barker, J.S.F.; Frydenberg, Jane; González, J.;

    2009-01-01

    variation for 15 microsatellite loci in each of nine populations in eastern Australia was used to estimate the size of the bottleneck, and to determine if any of these microsatellites marked genomic regions subject to recent selection. We estimate that on its introduction to Australia, D. buzzatii went...

  17. Isolation of novel microsatellite loci in the black goby Gobius niger and cross-amplification in other gobiid species (Perciformes, Gobiidae).

    Science.gov (United States)

    Ruggeri, P; Splendiani, A; Giovannotti, M; Nisi Cerioni, P; Caputo, V

    2012-11-01

    Twelve microsatellite loci were isolated from and characterized for the black goby Gobius niger. These loci were tested on a total of 48 individuals from two geographically distant locations (Orbetello and Cattolica) and the number of alleles ranged from two to 18, with expected (H(e)) and observed (H(o)) heterozygosities ranging from 0.042 to 0.941 and from 0.042 to 0.917, respectively. The loci described were used to cross-amplify other gobiid species belonging to Gobius, Zosterisessor, Lesueurigobius and Aphia.

  18. Isolation and characterization of 19 polymorphic microsatellite loci from the topmouth gudgeon, Pseudorasbora parva.

    Science.gov (United States)

    Zeng, C; Gul, Y; Yang, K; Cui, L; Wang, W-M; Gao, Z-X

    2011-01-01

    The Asiatic topmouth gudgeon, Pseudorasbora parva, is recognized as one of the most invasive fish species in many countries outside of Asia. We isolated and characterized 19 microsatellite loci from P. parva. The polymorphism of these 19 loci was tested on 40 individuals of P. parva sampled from a wild population located in Ezhou, Hubei province of China. The loci had 5 to 11 alleles, with a mean of 7.7 at each locus; 11 loci conformed to Hardy-Weinberg equilibrium. The expected and observed heterozygosities ranged from 0.237 to 0.973 and from 0.647 to 0.914, respectively. All microsatellite loci were in linkage equilibrium. These microsatellite markers are potentially useful for the assessment of population genetic structure during invasion and dispersal of P. parva in new habitats.

  19. Microsatellite flanking region similarities among different loci within insect species.

    Science.gov (United States)

    Meglécz, E; Anderson, S J; Bourguet, D; Butcher, R; Caldas, A; Cassel-Lundhagen, A; d'Acier, A C; Dawson, D A; Faure, N; Fauvelot, C; Franck, P; Harper, G; Keyghobadi, N; Kluetsch, C; Muthulakshmi, M; Nagaraju, J; Patt, A; Péténian, F; Silvain, J-F; Wilcock, H R

    2007-04-01

    Although microsatellites are ubiquitous in eukaryota, the number of available markers varies strongly among taxa. This meta-analysis was conducted on 32 insect species. Sequences were obtained from two assembled whole genomes, whole genome shotgun (WGS) sequences from 10 species and screening partial genomic libraries for microsatellites from 23 species. We have demonstrated: (1) strong differences in the abundance of microsatellites among species; (2) that microsatellites within species are often grouped into families based on similarities in their flanking sequences; (3) that the proportion of microsatellites grouped into families varies strongly among taxa; and (4) that microsatellite families were significantly more often associated with transposable elements - or their remnants - than unique microsatellite sequences.

  20. Microsatellite loci for tucumã of Amazonas (Astrocaryum aculeatum) and amplification in other Arecaceae.

    Science.gov (United States)

    Ramos, Santiago L Ferreyra; de Macêdo, Jeferson L Vasconcelos; Lopes, Maria T Gomes; Batista, Jacqueline S; Formiga, Kyara M; da Silva, Perla Pimentel; Saulo-Machado, Antonio C; Veasey, Elizabeth Ann

    2012-12-01

    Microsatellite loci were developed for tucumã of Amazonas (Astrocaryum aculeatum), and cross-species amplification was performed in six other Arecaceae, to investigate genetic diversity and population structure and to provide support for natural populations management. • Fourteen microsatellite loci were isolated from a microsatellite-enriched genomic library and used to characterize two wild populations of tucumã of Amazonas (Manaus and Manicoré cities). The investigated loci displayed high polymorphism for both A. aculeatum populations, with a mean observed heterozygosity of 0.498. Amplification rates ranging from 50% to 93% were found for four Astrocaryum species and two additional species of Arecaceae. • The information derived from the microsatellite markers developed here provides significant gains in conserved allelic richness and supports the implementation of several molecular breeding strategies for the Amazonian tucumã.

  1. Interpretation of electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx.

    Science.gov (United States)

    Arif, I A; Khan, H A; Shobrak, M; Al Homaidan, A A; Al Sadoon, M; Al Farhan, A H; Bahkali, A H

    2010-02-09

    Microsatellite markers are commonly used for examining population structure, especially inbreeding, outbreeding and gene flow. An array of microsatellite loci, preferably with multiallelic presentation, is preferable for ensuring accurate results. However, artifact peaks or stutters in the electrophoretograms significantly hamper the reliable interpretation of genotypes. We interpreted electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx. All the alleles of different loci exhibited good peak resolutions and hence were clearly identified. Moreover, none of the stutter peaks impaired the recognition or differentiation between homozygote and heterozygote. Our findings suggest that correct identification of alleles in the presence of co-amplified nonspecific fragments is important for reliable interpretation of microsatellite data.

  2. Development of Microsatellite Loci for the Riparian Tree Species Melaleuca argentea (Myrtaceae Using 454 Sequencing

    Directory of Open Access Journals (Sweden)

    Paul G. Nevill

    2013-05-01

    Full Text Available Premise of the study: Microsatellite primers were developed for Melaleuca argentea (Myrtaceae to evaluate genetic diversity and population genetic structure of this broadly distributed northern Australian riparian tree species. Methods and Results: 454 GS-FLX shotgun sequencing was used to obtain 5860 sequences containing putative microsatellite motifs. Two multiplex PCRs were optimized to genotype 11 polymorphic microsatellite loci. These loci were screened for variation in individuals from two populations in the Pilbara region, northwestern Western Australia. Overall, observed heterozygosities ranged from 0.27 to 0.86 (mean: 0.52 and the number of alleles per locus ranged from two to 13 (average: 4.3. Conclusions: These microsatellite loci will be useful in future studies of the evolutionary history and population and spatial genetic structure in M. argentea, and inform the development of seed sourcing strategies for the species.

  3. Isolation and characterization of microsatellite loci in the whale shark (Rhincodon typus)

    Science.gov (United States)

    Ramirez-Macias, D.; Shaw, K.; Ward, R.; Galvan-Magana, F.; Vazquez-Juarez, R.

    2009-01-01

    In preparation for a study on population structure of the whale shark (Rhincodon typus), nine species-specific polymorphic microsatellite DNA markers were developed. An initial screening of 50 individuals from Holbox Island, Mexico found all nine loci to be polymorphic, with two to 17 alleles observed per locus. Observed and expected heterozygosity per locus ranged from 0.200 to 0.826 and from 0.213 to 0.857, respectively. Neither statistically significant deviations from Hardy–Weinberg expectations nor statistically significant linkage disequilibrium between loci were observed. These microsatellite loci appear suitable for examining population structure, kinship assessment and other applications.

  4. Thousands of microsatellite loci from the venomous coralsnake (Micrurus fulvius) and variability of select loci across populations and related species

    Science.gov (United States)

    Castoe, Todd A.; Streicher, Jeffrey W.; Meik, Jesse M.; Ingrasci, Matthew J.; Poole, Alexander W.; de Koning, A.P. Jason; Campbell, Jonathan A.; Parkinson, Christopher L.; Smith, Eric N.; Pollock, David D.

    2012-01-01

    Studies of population genetics increasingly use next-generation DNA sequencing to identify microsatellite loci in non-model organisms. There are, however, relatively few studies that validate the feasibility of transitioning from marker development to experimental application across populations and species. North American coralsnakes of the Micrurus fulvius species complex occur in the United States and Mexico, and little is known about their population structure and phylogenetic relationships. This absence of information and population genetics markers is particularly concerning because they are highly venomous and have important implications on human health. To alleviate this problem in coralsnakes, we investigated the feasibility of using 454 shotgun sequences for microsatellite marker development. First, a genomic shotgun library from a single individual was sequenced (~7.74 megabases; 26,831 reads) to identify potentially amplifiable microsatellite loci (PALs). We then hierarchically sampled 76 individuals from throughout the geographic distribution of the species complex and examined whether PALs were amplifiable and polymorphic. Approximately half of the loci tested were readily amplifiable from all individuals, and 80% of the loci tested for variation were variable and thus informative as population genetic markers. To evaluate the repetitive landscape characteristics across multiple snakes, we also compared microsatellite content between the coralsnake and two other previously sampled snakes, the venomous copperhead (Agkistrodon contortrix) and Burmese python (Python molurus). PMID:22938699

  5. Thousands of microsatellite loci from the venomous coralsnake Micrurus fulvius and variability of select loci across populations and related species.

    Science.gov (United States)

    Castoe, Todd A; Streicher, Jeffrey W; Meik, Jesse M; Ingrasci, Matthew J; Poole, Alexander W; de Koning, A P Jason; Campbell, Jonathan A; Parkinson, Christopher L; Smith, Eric N; Pollock, David D

    2012-11-01

    Studies of population genetics increasingly use next-generation DNA sequencing to identify microsatellite loci in nonmodel organisms. There are, however, relatively few studies that validate the feasibility of transitioning from marker development to experimental application across populations and species. North American coralsnakes of the Micrurus fulvius species complex occur in the United States and Mexico, and little is known about their population structure and phylogenetic relationships. This absence of information and population genetics markers is particularly concerning because they are highly venomous and have important implications on human health. To alleviate this problem in coralsnakes, we investigated the feasibility of using 454 shotgun sequences for microsatellite marker development. First, a genomic shotgun library from a single individual was sequenced (approximately 7.74 megabases; 26,831 reads) to identify potentially amplifiable microsatellite loci (PALs). We then hierarchically sampled 76 individuals from throughout the geographic distribution of the species complex and examined whether PALs were amplifiable and polymorphic. Approximately half of the loci tested were readily amplifiable from all individuals, and 80% of the loci tested for variation were variable and thus informative as population genetic markers. To evaluate the repetitive landscape characteristics across multiple snakes, we also compared microsatellite content between the coralsnake and two other previously sampled snakes, the venomous copperhead (Agkistrodon contortrix) and Burmese python (Python molurus). © 2012 Blackwell Publishing Ltd.

  6. Polymorphic microsatellite loci identified through development and cross-species amplification within shorebirds

    Science.gov (United States)

    Williams, I.; Guzzetti, B.M.; Gust, Judy R.; Sage, G.K.; Gill, R.E.; Tibbitts, T.L.; Sonsthagen, S.A.; Talbot, S.L.

    2012-01-01

    We developed microsatellite loci for demographic assessments of shorebirds, a group with limited markers. First, we isolated five dinucleotide repeat microsatellite loci from the Black Oystercatcher (Haematopodidae: Haematopus bachmani), and three from the Bristle-thighed Curlew (Scolopacidae: Numenius tahitiensis); both species are of conservation concern. All eight loci were polymorphic in their respective target species. Hbaμ loci were characterized by two to three alleles with observed heterozygosity ranging from 0.07 to 0.33, and two to nine alleles were detected for Nut loci with observed heterozygosity ranging from 0.08 to 0.72. No linkage disequilibrium or departures from Hardy–Weinberg equilibrium were observed. The eight loci were also tested for cross-species amplification in 12 other species within Charadriidae and Scolopacidae, and the results demonstrated transferability across several genera. We further tested all 14 species at 12 additional microsatellite markers developed for other shorebirds: Dunlin (Calidris alpina; four loci) and Ruff (Philomachus pugnax; eight loci). Two markers (Hbaμ4 and Ruff6) were polymorphic in 13 species, while two (Calp6 and Ruff9) were monomorphic. The remaining eight markers revealed polymorphism in one to nine species each. Our results provide further evidence that locus Ruff10 is sex-linked, contrary to the initial description. These markers can be used to enhance our understanding of shorebird biology by, for example, helping to determine migratory connectivity among breeding and wintering populations and detecting relatedness among individuals.

  7. Microsatellite loci and peroxidase alleles correlation in somaclonal ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-07-19

    Jul 19, 2010 ... POD is affected by environmental factors, genotype and their interaction. It is considered to ..... University of Ireland, Ph.D. thesis pp. 1-200. Brondani .... Elymus species using wheat microsatellite markers and RAPD markers.

  8. Isolation and characterization of 10 microsatellite loci in Cneorum tricoccon (Cneoraceae), a Mediterranean relict plant.

    Science.gov (United States)

    García-Fernández, Alfredo; Lázaro-Nogal, Ana; Traveset, Anna; Valladares, Fernando

    2012-08-01

    The main aim of this study was to isolate and characterize microsatellite loci in Cneorum tricoccon (Cneoraceae), a Mediterranean shrub relict of the early Tertiary, which inhabits western Mediterranean islands and coasts. Microsatellites will be useful for investigating biogeography and landscape genetics across the species distribution range, including current or past gene flow. Seventeen microsatellite loci were characterized, of which 10 were polymorphic and amplified for a total of 56 alleles in three populations of C. tricoccon. The markers revealed average coefficients of expected heterozygosity (H(e) = 0.425), observed heterozygosity (H(o) = 0.282), and inbreeding coefficient value per population (F(IS) = 0.408). These microsatellite primers will potentially be useful in the study of population and landscape genetics, conservation status of isolated populations, island-continental distribution, current or historical movements between populations, and in the investigation of the consequences of dispersal mechanisms of these plants.

  9. Isolation and characterization of 32 microsatellite loci for topmouth culter (Culter alburnus Basilewsky).

    Science.gov (United States)

    Liu, S-L; Gu, Z-M; Jia, Y-Y; Zhao, J-L; Jiang, W-P; Li, Q; Li, F

    2014-09-12

    The topmouth culter (Culter alburnus) is an economically important freshwater fish, which is widely distributed throughout large rivers, reservoirs, and lake areas of China. We report here the isolation and characterization of 32 new polymorphic microsatellite loci isolated from genomic DNA in this species enriched by (CA)12 and (GA)12 probes. The variability of these microsatellites was tested on 30 individuals cultured. The average allele number was 6.6 per locus, ranging from 3 to 12. The observed heterozygosity was from 0.4667 to 0.9000, and the expected heterozygosity was from 0.6163 to 0.9085. After using Bonferroni's correction for multiple tests, there was no evidence of linkage disequilibrium between pairs of loci, but deviations from Hardy-Weinberg equilibrium were found in 3 loci. These microsatellites can be used to study QTL of economic importance, population genetic diversity and the construction of genetic maps for C. alburnus in the future.

  10. Isolation and characterization of microsatellite loci in the common milkweed, Asclepias syriaca (Apocynaceae).

    Science.gov (United States)

    Kabat, Susan M; Dick, Christopher W; Hunter, Mark D

    2010-05-01

    Microsatellite primers were developed for the common milkweed, Asclepias syriaca L., to assist in genet identification and the analysis of spatial genetic structure. Using an enrichment cloning protocol, eight microsatellite loci were isolated and characterized in a Michigan population of A. syriaca. The primers amplified di- and trinucleotide repeats with 4-13 alleles per locus. The primers will be useful for studies of clonality and gene flow in natural populations.

  11. Characterization of new microsatellite loci for population genetic studies in the Smooth Cauliflower Coral (Stylophora sp.)

    KAUST Repository

    Banguera-Hinestroza, E.

    2013-01-09

    A total of one hundred microsatellites loci were selected from the draft genome of Stylophora pistillata and evaluated in previously characterized samples of Stylophora cf pistillata from the Red Sea. 17 loci were amplified successfully and tested in 24 individuals from samples belonging to a single population from the central region of the Red Sea. The number of alleles ranged from 3 to 15 alleles per locus, while observed heterozygosity ranged from 0. 292 to 0. 95. Six of these loci showed significant deviations from Hardy-Weinberg equilibrium (HWE) expectations, and 4/136 paired loci comparisons suggested linkage disequilibrium after Bonferroni corrections. After excluding loci with significant HWE deviation and evidence of null alleles, average genetic diversity over loci in the population studied (N = 24, Nloci = 11) was 0. 701 ± 0. 380. This indicates that these loci can be used effectively to evaluate genetic diversity and undertake population genetics studies in Stylophora sp. populations. 2013 The Author(s).

  12. Characterisation and cross-amplification of polymorphic microsatellite loci in ant-associated root-aphids

    DEFF Research Database (Denmark)

    Ivens, A.B.F.; Kronauer, Daniel Jan Christoph; Boomsma, J.J.

    2011-01-01

    Twenty-six polymorphic microsatellite loci were developed for four species of ant-associated root-aphids: Geoica utricularia, Forda marginata, Tetraneura ulmi and Anoecia corni. We found up to 9 alleles per locus, with an average of 4.8. We also report polymorphic cross-amplification of eleven...... of these markers between different pairs of study species. Furthermore, we tested previously published aphid microsatellites and found one locus developed for Pemphigus bursarius to be polymorphic in G. utricularia. These microsatellite markers will be useful to study the population structure of aphids associated...

  13. Development of microsatellite loci for the invasive weed Wedelia trilobata (Asteraceae).

    Science.gov (United States)

    Wu, Wei; Zhou, Ren-Chao; Huang, Hui-Run; Ge, Xue-Jun

    2010-11-01

    Microsatellite markers were developed to help elucidate the population genetics of the invasive species Wedelia trilobata. • Using the Fast Isolation by AFLP of Sequences COntaining (FIASCO) repeats protocol, 23 sets of primers for amplifying microsatellite loci were identified in W. trilobata, 10 of which showed polymorphism (two to five alleles per locus) in samples of two populations of W. trilobata, one from China and one from Peru. Six of these loci were successfully amplified from samples of the native congener W. chinensis, with expected sizes. • These markers may be useful for further investigation of population genetics of Wedelia trilobata and other congener species.

  14. Isolation and characterization of polymorphic microsatellite loci in the green leafhopper Empoasca vitis Goethe (Homoptera).

    Science.gov (United States)

    Papura, D; Giresse, X; Chauvin, B; Caron, H; Delmotte, F; VAN Helden, M

    2009-05-01

    Eight dinucleotide microsatellite loci were isolated and characterized within the green leafhopper Empoasca vitis (Goethe) using an enrichment cloning procedure. Primers were tested on 171 individuals collected in the southwest of France from the vine plants. The identified loci were polymorphic, with allelic diversity ranging from two to 18 alleles per locus. Observed heterozygosities were from 0.021 to 0.760. These microsatellite markers should prove to be a useful tool for estimating the population genetic structure, host-plant specialization and migration capacity of this insect.

  15. Isolation and characterization of microsatellite loci from the tick Amblyomma aureolatum (Acari: Ixodidae).

    Science.gov (United States)

    Ogrzewalska, M; Bajay, M M; Schwarcz, K; Bajay, S K; Telles, M P C; Pinheiro, J B; Zucchi, M I; Pinter, A; Labruna, M B

    2014-11-14

    Amblyomma aureolatum (Pallas) is the main vector of the bacterium Rickettsia rickettsii, the etiological agent of Brazilian spotted fever. This disease is the most lethal human spotted fever rickettsiosis in the world. Microsatellite loci were isolated from a dinucleotide-enriched library produced from A. aureolatum sampled in Southeastern Brazil. Eight polymorphic microsatellites were further characterized among 38 individuals sampled from São Paulo metropolitan region. The number of observed alleles ranged from 2 to 9, observed heterozygosity was 0.184-0.647, and expected heterozygosity was 0.251-0.747. Cross-species amplifications suggested that these loci will be useful for other Amblyomma species.

  16. Microsatellite Loci for Orthophytum ophiuroides (Bromelioideae, Bromeliaceae Species Adapted to Neotropical Rock Outcrops

    Directory of Open Access Journals (Sweden)

    Felipe Aoki-Gonçalves

    2014-03-01

    Full Text Available Premise of the study: Microsatellite primers were developed for Orthophytum ophiuroides, a rupicolous bromeliad species endemic to neotropical rocky fields. These microsatellite loci will be used to investigate population differentiation and species cohesion in such fragmented environments. The loci were tested for cross-amplification in related bromeliad species. Methods and Results: Eleven polymorphic microsatellite markers were isolated and characterized from an enriched library of O. ophiuroides. The loci were tested on 42 individuals from two populations of this species. The number of alleles per locus ranged from three to nine and the expected and observed heterozygosities ranged from 0.167 to 0.870 and from 0.369 to 0.958, respectively. Seven loci successfully amplified in other related bromeliad species. Conclusions: Our results suggest that the microsatellite loci developed here will be useful to assess genetic diversity and gene flow in O. ophiuroides for the investigation of population differentiation and species cohesion in neotropical mountainous habitats.

  17. Microsatellite loci for population and parentage analysis in the Amazon River dolphin (Inia geoffrensis de Blainville, 1817).

    Science.gov (United States)

    Gravena, Waleska; Hrbek, Tomas; DA Silva, Vera M S; Astolfi-Filho, Spartaco; Farias, Izeni P

    2009-03-01

    We developed specific primers for microsatellite DNA regions for the Amazon River dolphin or boto Inia geoffrensis, for use in population and conservation genetic studies. We also tested their transferability for two other species, Pontoporia blainvillei (sister taxon of I. geoffrensis) and Sotalia guianensis. A total of 12 microsatellite loci were polymorphic for the boto. An additional 25 microsatellite loci previously isolated from other cetacean species were also tested in the boto. The 26 polymorphic microsatellite loci indicate they will be excellent markers for studies of population structure and kinship relations of the boto.

  18. Development and characterization of thirteen microsatellite loci in Clark's nutcracker (Nucifraga columbiana)

    Science.gov (United States)

    Oyler-McCance, Sara J.; Fike, Jennifer A.; Castoe, Todd A.; Tomback, Diana F.; Wunder, Michael B.; Schaming, Taza D.

    2013-01-01

    Clark’s nutcrackers are important seed dispersers for two widely-distributed western North American conifers, whitebark pine and limber pine, which are declining due to outbreaks of mountain pine beetle and white pine blister rust. Because nutcracker seed dispersal services are key to maintaining viable populations of these imperiled pines, knowledge of movement patterns of Clark’s nutcrackers helps managers understand local extinction risks for these trees. To investigate population structure within Clark’s nutcracker, we developed primers for and characterized 13 polymorphic microsatellite loci. In a screen of 22 individuals from one population, levels of variability ranged from 6 to 15 alleles. No loci were found to be linked, although 4 loci revealed significant departures from Hardy–Weinberg equilibrium and evidence of null alleles. These microsatellite loci will enable population genetic analyses of Clark’s nutcrackers, which could provide insights into the spatial relationships between nutcrackers and the trees they help disperse.

  19. Development and characterization of microsatellite loci for the haploid-diploid red seaweed Gracilaria vermiculophylla.

    Science.gov (United States)

    Kollars, Nicole M; Krueger-Hadfield, Stacy A; Byers, James E; Greig, Thomas W; Strand, Allan E; Weinberger, Florian; Sotka, Erik E

    2015-01-01

    Microsatellite loci are popular molecular markers due to their resolution in distinguishing individual genotypes. However, they have rarely been used to explore the population dynamics in species with biphasic life cycles in which both haploid and diploid stages develop into independent, functional organisms. We developed microsatellite loci for the haploid-diploid red seaweed Gracilaria vermiculophylla, a widespread non-native species in coastal estuaries of the Northern hemisphere. Forty-two loci were screened for amplification and polymorphism. Nine of these loci were polymorphic across four populations of the extant range with two to eleven alleles observed. Mean observed and expected heterozygosities ranged from 0.265 to 0.527 and 0.317 to 0.387, respectively. Overall, these markers will aid in the study of the invasive history of this seaweed and further studies on the population dynamics of this important haploid-diploid primary producer.

  20. Development and characterization of microsatellite loci for the haploid–diploid red seaweed Gracilaria vermiculophylla

    Science.gov (United States)

    Byers, James E.; Greig, Thomas W.; Strand, Allan E.; Weinberger, Florian

    2015-01-01

    Microsatellite loci are popular molecular markers due to their resolution in distinguishing individual genotypes. However, they have rarely been used to explore the population dynamics in species with biphasic life cycles in which both haploid and diploid stages develop into independent, functional organisms. We developed microsatellite loci for the haploid–diploid red seaweed Gracilaria vermiculophylla, a widespread non-native species in coastal estuaries of the Northern hemisphere. Forty-two loci were screened for amplification and polymorphism. Nine of these loci were polymorphic across four populations of the extant range with two to eleven alleles observed. Mean observed and expected heterozygosities ranged from 0.265 to 0.527 and 0.317 to 0.387, respectively. Overall, these markers will aid in the study of the invasive history of this seaweed and further studies on the population dynamics of this important haploid–diploid primary producer. PMID:26339541

  1. Development and characterization of microsatellite loci for the haploid–diploid red seaweed Gracilaria vermiculophylla

    Directory of Open Access Journals (Sweden)

    Nicole M. Kollars

    2015-08-01

    Full Text Available Microsatellite loci are popular molecular markers due to their resolution in distinguishing individual genotypes. However, they have rarely been used to explore the population dynamics in species with biphasic life cycles in which both haploid and diploid stages develop into independent, functional organisms. We developed microsatellite loci for the haploid–diploid red seaweed Gracilaria vermiculophylla, a widespread non-native species in coastal estuaries of the Northern hemisphere. Forty-two loci were screened for amplification and polymorphism. Nine of these loci were polymorphic across four populations of the extant range with two to eleven alleles observed. Mean observed and expected heterozygosities ranged from 0.265 to 0.527 and 0.317 to 0.387, respectively. Overall, these markers will aid in the study of the invasive history of this seaweed and further studies on the population dynamics of this important haploid–diploid primary producer.

  2. Eleven Novel Polymorphic Microsatellite Loci for Oval Squid Sepioteuthis Lessoniana (Shiro-Ika Type)

    Science.gov (United States)

    Tomano, Satoshi; Ahmad-Syazni, Kamarudin; Ueta, Yukio; Ohara, Kenichi; Umino, Tetsuya

    2013-01-01

    The oval squid Sepioteuthis lessoniana is one of the most economically important squid species in Japan; however, its population structure is poorly understood due to the lack of hypervariable markers. Such information is critical for managing sustainable fisheries, as well as for ensuring the existence of wild S. lessoniana stocks. Eleven candidate microsatellite loci were isolated from a small insert genomic DNA library. Polymorphisms in these 11 loci were screened in 24 wild individuals. The number of alleles per locus was found to range from 5 to 19 alleles, and the observed heterozygosity ranged from 0.292 to 0.958. No evidence for linkage disequilibrium was detected among all the loci. The genotypic proportions conformed to Hardy-Weinberg equilibrium, except at one locus. In conclusion, these polymorphic microsatellite loci may be used to develop a genetic framework to manage S. lessoniana in the future. PMID:24108369

  3. Characterization of 11 new microsatellite loci in taro (Colocasia esculenta).

    Science.gov (United States)

    Hu, Kan; Huang, Xing Fang; Ke, Wei Dong; Ding, Yi

    2009-03-01

    Eleven new microsatellite markers were isolated from taro, Colocasia esculenta (L.) Schott, a root crop widely distributed all over the world. Forty-eight primer pairs were designed from a microsatellite-enriched genomic library, of which 11 primer pairs have polymorphisms in 30 individuals tested from a population in China, which revealed two to six alleles per locus with the observed and expected heterozygosity levels ranging from 0 to 0.733 and from 0.381 to 0.731, respectively. These new genetic markers will be useful for the study of taro germplasm management and population evolution in the future.

  4. Development and characterization of 11 microsatellite loci for the Mona Island iguana (Cyclura cornuta stejnegeri)

    OpenAIRE

    Pérez-Buitrago, Néstor; Rosas G., Keysa; Acevedo-Rodríguez,Pedro; Funk, S. M.; McMillan, Owen

    2008-01-01

    We isolated and characterized 11 microsatellite loci in the Mona Island iguana (Cyclura cornuta stejnegeri). Eleven loci exhibit moderate to high allelic diversity (two to 12 alleles, mean = 4.5) and polymorphism (mean observed heterozygosity, 0.56; range, 0.26 to 0.78) in 41 adults. This marker set has low probability of identity and high parentage exclusion power and will be suitable for studies of paternity, social organization and relatedness in this species.

  5. Thousands of microsatellite loci from the venomous coralsnake (Micrurus fulvius) and variability of select loci across populations and related species

    OpenAIRE

    Castoe, Todd A.; Streicher, Jeffrey W.; Jesse M Meik; Ingrasci, Matthew J.; Poole, Alexander W.; de Koning, A. P. Jason; Campbell, Jonathan A.; Parkinson, Christopher L; Eric N. Smith; Pollock, David D.

    2012-01-01

    Studies of population genetics increasingly use next-generation DNA sequencing to identify microsatellite loci in non-model organisms. There are, however, relatively few studies that validate the feasibility of transitioning from marker development to experimental application across populations and species. North American coralsnakes of the Micrurus fulvius species complex occur in the United States and Mexico, and little is known about their population structure and phylogenetic relationship...

  6. Isolation and Characterization of Microsatellite Loci in the Chinese Cobra Naja atra (Elapidae

    Directory of Open Access Journals (Sweden)

    Xiang Ji

    2011-07-01

    Full Text Available We characterize thirteen polymorphic microsatellite loci isolated from Naja atra genomic libraries, which were enriched for AC-motif microsatellites. The thirteen loci were screened on a group of 48 individuals from two populations, one in Yong’an and the other in Ganzhou. These markers revealed a relatively high degree of genetic diversity (4–12 alleles per locus and heterozygosity (Ho ranged from 0.213–0.854 and He ranged from 0.301–0.838. Tests for departure from Hardy-Weinberg equilibrium and for linkage disequilibrium were conducted for each of the two populations separately. After sequential Bonferroni correction, none of the 13 loci showed significant departures from Hardy-Weinberg equilibrium. Hierarchical analysis of molecular variance indicated that a small but significant (P < 0.001 proportion (16.0% of the total variation in the microsatellite DNA data were attributable to differences among populations, indicating geographical structuring and restricted gene flow. It could be attributable to the Wuyi mountains in the area having a sufficiently isolating effect to significantly reduce gene flow. Our microsatellite data also showed a low Nm (1.31 value in the two populations from mainland China. Thus, the Yong’an and Ganzhou populations could be treated as distinct evolutionarily significant units (ESUs. The high level of polymorphism revealed by these microsatellite markers will be useful for the study of gene flow, population structure and evolutionary history of N. atra.

  7. Isolation and characterization of microsatellite loci in the Chinese Cobra Naja atra (Elapidae).

    Science.gov (United States)

    Lin, Long-Hui; Mao, Lu-Xi; Luo, Xia; Qu, Yan-Fu; Ji, Xiang

    2011-01-01

    We characterize thirteen polymorphic microsatellite loci isolated from Naja atra genomic libraries, which were enriched for AC-motif microsatellites. The thirteen loci were screened on a group of 48 individuals from two populations, one in Yong'an and the other in Ganzhou. These markers revealed a relatively high degree of genetic diversity (4-12 alleles per locus) and heterozygosity (Ho ranged from 0.213-0.854 and He ranged from 0.301-0.838). Tests for departure from Hardy-Weinberg equilibrium and for linkage disequilibrium were conducted for each of the two populations separately. After sequential Bonferroni correction, none of the 13 loci showed significant departures from Hardy-Weinberg equilibrium. Hierarchical analysis of molecular variance indicated that a small but significant (P < 0.001) proportion (16.0%) of the total variation in the microsatellite DNA data were attributable to differences among populations, indicating geographical structuring and restricted gene flow. It could be attributable to the Wuyi mountains in the area having a sufficiently isolating effect to significantly reduce gene flow. Our microsatellite data also showed a low N(m) (1.31) value in the two populations from mainland China. Thus, the Yong'an and Ganzhou populations could be treated as distinct evolutionarily significant units (ESUs). The high level of polymorphism revealed by these microsatellite markers will be useful for the study of gene flow, population structure and evolutionary history of N. atra.

  8. Isolation and characterization of 108 novel microsatellite loci for Atlantic coastal killifish (Fundulus heteroclitus)

    Science.gov (United States)

    We characterized 108 polymorphic microsatellite loci for the mummichog (Fundulus heteroclitus), an Atlantic coastal killifish. Allelic diversity among 26 individuals ranged between 2 and 15 alleles per locus, while expected heterozygosity ranged from 0.075 to 0.904. Significant ...

  9. CHARACTERIZATION OF SEVEN POLYMORPHIC MICROSATELLITE LOCI IN THE COMMON LOON (GAVIA IMMER)

    Science.gov (United States)

    We describe polymerase chain reaction (PCR) primers and conditions to amplify seven microsatellite DNA loci isolated from the Common Loon (Gavia immer). The PCR primers were tested on 83 individuals from ten locations in North America, including breeding, migration stopover, and...

  10. Characterization of microsatellite loci in the marine seaweeds, Fucus serratus and F-evanescens (Heterokontophyta; Fucaceae)

    NARCIS (Netherlands)

    Coyer, JA; Veldsink, JH; Jones, K; Stam, WT; Olsen, JL

    2002-01-01

    Fucus serratus and F. evanescens commonly occur on Northern European shores. Nine microsatellite loci were developed for F. serratus (8-22 alleles, observed heterozygosities = 0.367-0.850) and one for F. evanescens (seven alleles, observed heterozygosity = 0.804). Cross-amplification was apparent, a

  11. Characterization of microsatellite loci in the marine seaweed Ascophyllum nodosum (Phaeophyceae; Fucales)

    NARCIS (Netherlands)

    Olsen, JL; Sadowski, G; Stam, WT; Veldsink, JH; Jones, K

    Ascophyllum nodosum L. dominates rocky intertidal shores throughout the temperate North Atlantic. Six microsatellite loci were developed for A. nodosum using enriched libraries. The number of alleles ranged from 9 to 24 and heterozygosities from 0.2213 to 0.7785. Ascophyllum is monotypic. There was

  12. Characterization of microsatellite loci in the marine seaweeds, Fucus serratus and F-evanescens (Heterokontophyta; Fucaceae)

    NARCIS (Netherlands)

    Coyer, J.A.; Veldsink, J.H.; Jones, K.; Stam, W.T.; Olsen, J.L.

    Fucus serratus and F. evanescens commonly occur on Northern European shores. Nine microsatellite loci were developed for F. serratus (8-22 alleles, observed heterozygosities = 0.367-0.850) and one for F. evanescens (seven alleles, observed heterozygosity = 0.804). Cross-amplification was apparent,

  13. Dinucleotide microsatellite DNA loci from the ant Myrmica scabrinodis

    DEFF Research Database (Denmark)

    Zeisset, Inga; Ebsen, Jon R.; Boomsma, Jacobus Jan

    2005-01-01

    We describe the isolation and characterization of five dinucleotide microsatellite loci in the ant Myrmica scabrinodis, which were obtained using a magnetic bead hybridization selection protocol. The PCR primers were tested on nine to 11 individuals. The number of alleles ranged from two to 13, a...

  14. Development and characterization of microsatellite loci for common raven (Corvus corax) and cross species amplification in other Corvidae

    OpenAIRE

    Pruett, Christin L.; Wan, Leping; Li, Tianyu; Spern, Cory; Lance, Stacey L.; Glenn, Travis; Faircloth, Brant; Winker, Kevin

    2015-01-01

    Background A priority for conservation is the identification of endemic populations. We developed microsatellite markers for common raven (Corvus corax), a bird species with a Holarctic distribution, to identify and assess endemic populations in Alaska. Results From a total of 50 microsatellite loci, we isolated and characterized 15 loci. Eight of these loci were polymorphic and readily scoreable. Eighteen to 20 common ravens from Fairbanks, Alaska were genotyped showing the following variabi...

  15. Alelle number and heterozigosity for microsatellite loci in different stingless bee species (Hymenoptera: Apidae, Meliponini).

    Science.gov (United States)

    Francisco, Flávio de O; Brito, Rute M; Arias, Maria C

    2006-01-01

    In the present study we compare genetic characteristics (allele diversity and observed heterozygosity) of microsatellite loci, from three stingless bee species (Plebeia remota Holmberg, Partamona mulata Moure In Camargo and Partamona helleri Friese), amplified by using heterospecific primers originally designed for Melipona bicolor Lepeletier and Scaptotrigona postica Latreille. We analyzed 360 individuals of P. remota from 72 nests, 58 individuals of R. mulata from 58 nests, and 47 individuals of P. helleri from 47 nests. The three species studied showed low level of polymorphism for the loci amplified with primers derived from M. bicolor. However, for the loci amplified with primers derived from S. postica, only P. remota presented low level of polymorphism.

  16. Isolation and characterization of microsatellite loci in the intertidal sponge Halichondria panicea

    Science.gov (United States)

    Knowlton, A.L.; Pierson, Barbara J.; Talbot, S.L.; Highsmith, R.C.

    2003-01-01

    GA- and CA-enriched genomic libraries were constructed for the intertidal sponge Halichondria panicea. Unique repeat motifs identified varied from the expected simple dinucleotide repeats to more complex repeat units. All sequences tended to be highly repetitive but did not necessarily contain the targeted motifs. Seven microsatellite loci were evaluated on sponges from the clone source population. All seven were polymorphic with 5.43??0.92 mean number of alleles. Six of the seven loci that could be resolved had mean heterozygosities of 0.14-0.68. The loci identified here will be useful for population studies.

  17. Development and characterization of eight polymorphic microsatellite loci from Pistacia lentiscus L. (Anacardiaceae).

    Science.gov (United States)

    Albaladejo, Rafael G; Sebastiani, F; Aparicio, A; Buonamici, A; González-Martínez, S C; Vendramin, G G

    2008-07-01

    We have developed a set of eight polymorphic nuclear microsatellite markers for the Mediterranean shrub Pistacia lentiscus by means of an enriched library method. Characterization for the eight loci was carried out on 42 individuals from two populations sampled in southern Spain. The overall number of alleles detected was 59, ranging from three to 13 per locus. Expected heterozygosity per locus and population ranged from 0.139 to 0.895. Two loci albeit only in one population (Seville) departed significantly from Hardy-Weinberg equilibrium expectations and no linkage disequilibrium between pairs of loci was detected. These markers will be used in studies of gene flow across a fragmented landscape.

  18. Development of microsatellite loci in Mediterranean sarsaparilla (Smilax aspera; Smilacaceae) using transcriptome data.

    Science.gov (United States)

    Qi, Zhe-Chen; Shen, Chao; Han, Yu-Wei; Shen, Wei; Yang, Man; Liu, Jinliang; Liang, Zong-Suo; Li, Pan; Fu, Cheng-Xin

    2017-04-01

    Although several microsatellite markers of Smilax aspera (Smilacaceae) have been reported in a previous study, due to universality issues in cross-population amplification, we have newly developed microsatellite markers for S. aspera based on transcriptome data to further investigate gene flow and genetic structure of its circum-Mediterranean, East African, and South Asian populations. A total of 4854 simple sequence repeat (SSR) primer pairs were designed from 99,193 contigs acquired from public transcriptome data of S. bona-nox. Forty-six microsatellite loci were selected for further genotyping in 12 S. aspera populations. The number of alleles varied from three to 28, and 93.5% of the developed microsatellite markers could be cross-amplified in least one of three congeneric Smilax species. The SSR markers developed in this study will facilitate further studies on genetic diversity and phylogeographic patterns of S. aspera in intercontinental geographical scales.

  19. MicNeSs: genotyping microsatellite loci from a collection of (NGS) reads.

    Science.gov (United States)

    Suez, Marie; Behdenna, Abdelkader; Brouillet, Sophie; Graça, Paula; Higuet, Dominique; Achaz, Guillaume

    2016-03-01

    Microsatellites are widely used in population genetics to uncover recent evolutionary events. They are typically genotyped using capillary sequencer, which capacity is usually limited to 9, at most 12 loci for each run, and which analysis is a tedious task that is performed by hand. With the rise of next-generation sequencing (NGS), a much larger number of loci and individuals are available from sequencing: for example, on a single run of a GS Junior, 28 loci from 96 individuals are sequenced with a 30X cover. We have developed an algorithm to automatically and efficiently genotype microsatellites from a collection of reads sorted by individual (e.g. specific PCR amplifications of a locus or a collection of reads that encompass a locus of interest). As the sequencing and the PCR amplification introduce artefactual insertions or deletions, the set of reads from a single microsatellite allele shows several length variants. The algorithm infers, without alignment, the true unknown allele(s) of each individual from the observed distributions of microsatellites length of all individuals. MicNeSs, a python implementation of the algorithm, can be used to genotype any microsatellite locus from any organism and has been tested on 454 pyrosequencing data of several loci from fruit flies (a model species) and red deers (a nonmodel species). Without any parallelization, it automatically genotypes 22 loci from 441 individuals in 11 hours on a standard computer. The comparison of MicNeSs inferences to the standard method shows an excellent agreement, with some differences illustrating the pros and cons of both methods.

  20. Polymorphic microsatellite loci for two Atlantic oyster species: Crassostrea rhizophorae and C. gasar.

    Science.gov (United States)

    Cavaleiro, Nathalia P; Solé-Cava, Antonio M; Lazoski, Cristiano; Cunha, Haydée A

    2013-12-01

    Using a CA/CAA enriched library screening procedure, we isolated and characterised a total of seventeen polymorphic microsatellite loci for two species of Crassostrea with recognised economic importance. Eleven microsatellite loci were developed for C. rhizophorae, a Western Atlantic species for which no microsatellites were previously known. Another six loci were developed for C. gasar, a species that occurs on both sides of the South Atlantic, adding to the ten loci previously described for the species. The levels of polymorphism were estimated using 24 C. rhizophorae from Southeast Brazil (São Paulo) and 23 C. gasar individuals from North Brazil (Maranhão). The number of alleles per polymorphic locus varied from 3 to 27, and the observed and expected heterozygosities ranged between 0.174 and 0.958 and between 0.237 and 0.972 in C. rhizophorae and C. gasar, respectively. No linkage disequilibrium was found between any locus pair, and four of them exhibited deviations from Hardy-Weinberg expectations. Of the 17 loci developed, 8 cross-amplified in C. gigas and 13 in C. virginica. These markers are useful for evolution and population genetics studies of Crassostrea species and may provide fundamental data for the future cultivation of native oysters in Western Atlantic.

  1. Isolation of 91 polymorphic microsatellite loci in the western Mediterranean endemic Carex helodes (Cyperaceae)1

    Science.gov (United States)

    Arroyo, Juan M.; Escudero, Marcial; Jordano, Pedro

    2016-01-01

    Premise of the study: Microsatellite primers were developed for Carex helodes (Cyperaceae), a western Mediterranean endemic that is locally distributed in southern Portugal and southwestern Spain and rare in northern Morocco. Methods and Results: One hundred nine nuclear microsatellite markers were developed using a shotgun pyrosequencing method, resulting in 91 polymorphic and 18 monomorphic loci when tested using 19 individuals sampled from five populations from Portugal, Spain, and Morocco. Loci averaged 3.23 alleles per locus (SD = 1.15). In a single population (Cortelha population, Portugal), the 34 most polymorphic loci showed a mean observed heterozygosity of 0.357 (SD = 0.292) and mean expected heterozygosity of 0.384 (SD = 0.255). Conclusions: Next-generation sequencing allowed us to develop a high number of genetic markers with levels of polymorphism adequate to study gene flow among populations. However, when genotyping the individuals within a population, we found low levels of variation. PMID:26819859

  2. Development and characterization of microsatellite loci for the endangered scrub lupine, Lupinus aridorum (Fabaceae)1

    Science.gov (United States)

    Ricono, Angela; Bupp, Glen; Peterson, Cheryl; Nunziata, Schyler O.; Lance, Stacey L.; Pruett, Christin L.

    2015-01-01

    Premise of the study: Microsatellite primers were developed in scrub lupine (Lupinus aridorum, Fabaceae), an endemic species to Florida that is listed as endangered in the United States, to assess connectivity among populations, identify hybrids, and examine genetic diversity. Methods and Results: We isolated and characterized 12 microsatellite loci polymorphic in scrub lupine or in closely related species (i.e., sky-blue lupine [L. diffusus] and Gulf Coast lupine [L. westianus]). Loci showed low to moderate polymorphism, ranging from two to 14 alleles per locus and 0.01 to 0.86 observed heterozygosity. Conclusions: These loci are the first developed for Florida species of lupine and will be used to determine differentiation among species and to aid in conservation of the endangered scrub lupine. PMID:25909046

  3. Development and characterization of microsatellite loci for the endangered scrub lupine, Lupinus aridorum (Fabaceae).

    Science.gov (United States)

    Ricono, Angela; Bupp, Glen; Peterson, Cheryl; Nunziata, Schyler O; Lance, Stacey L; Pruett, Christin L

    2015-04-01

    Microsatellite primers were developed in scrub lupine (Lupinus aridorum, Fabaceae), an endemic species to Florida that is listed as endangered in the United States, to assess connectivity among populations, identify hybrids, and examine genetic diversity. We isolated and characterized 12 microsatellite loci polymorphic in scrub lupine or in closely related species (i.e., sky-blue lupine [L. diffusus] and Gulf Coast lupine [L. westianus]). Loci showed low to moderate polymorphism, ranging from two to 14 alleles per locus and 0.01 to 0.86 observed heterozygosity. These loci are the first developed for Florida species of lupine and will be used to determine differentiation among species and to aid in conservation of the endangered scrub lupine.

  4. Allelic frequencies of two microsatellite loci in four populations of brown trout (Salmo trutta

    Directory of Open Access Journals (Sweden)

    EDIT VARDHAMI

    2014-06-01

    Full Text Available Two microsatellite loci, Str60Inra and Ssa197, were PCR amplified on 30 individuals for each populations of brown trout (Salmo trutta. A total of 120 individuals were selected from rivers of the Florence province (Italy, Valbona and Cen (Albania, Lepenci (Kosovo. There were identified 32 different alleles for Str60Inra and 41 for the locus Ssa197. Mean number of alleles ranged from 9 (Cen to 20.5 (Florence. The mean observed and expected heterosygosities values were 0.329 and 0.755, respectively. Both microsatellite loci were polymorphic. The highest value of heterozygosity was observed in Lepenci. Significant deviations from Hardy Weinberg were found in both loci.

  5. Genetic diversity and differentiation in reef-building Millepora species, as revealed by cross-species amplification of fifteen novel microsatellite loci

    Science.gov (United States)

    Planes, Serge; Zhou, Yuxiang; Berteaux-Lecellier, Véronique; Boissin, Emilie

    2017-01-01

    Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coral Millepora platyphylla, an important reef-builder of Indo-Pacific reefs. We tested the cross-species amplification of these loci in five other species of the genus Millepora and analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target species M. platyphylla, among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five other Millepora species revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean species M. complanata due to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species of Millepora. Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoan Millepora species creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs. PMID:28243525

  6. Development and characterization of microsatellite loci for Ocotea species (Lauraceae) threatened with extinction.

    Science.gov (United States)

    Martins, E M; Martinelli, G; Arbetman, M P; Lamont, R W; Simões-Araújo, J L; Powell, D; Ciampi-Guillardi, M; Baldauf, C; Quinet, A; Galisa, P; Shapcott, A

    2014-07-07

    The Atlantic rainforest species Ocotea catharinensis, Ocotea odorifera, and Ocotea porosa have been extensively harvested in the past for timber and oil extraction and are currently listed as threatened due to overexploitation. To investigate the genetic diversity and population structure of these species, we developed 8 polymorphic microsatellite markers for O. odorifera from an enriched microsatellite library by using 2 dinucleotide repeats. The microsatellite markers were tested for cross-amplification in O. catharinensis and O. porosa. The average number of alleles per locus was 10.2, considering all loci over 2 populations of O. odorifera. Observed and expected heterozygosities for O. odorifera ranged from 0.39 to 0.93 and 0.41 to 0.92 across populations, respectively. Cross-amplification of all loci was successfully observed in O. catharinensis and O. porosa except 1 locus that was found to lack polymorphism in O. porosa. Combined probabilities of identity in the studied Ocotea species were very low ranging from 1.0 x 10-24 to 7.7 x 10-24. The probability of exclusion over all loci estimated for O. odorifera indicated a 99.9% chance of correctly excluding a random nonparent individual. The microsatellite markers described in this study have high information content and will be useful for further investigations on genetic diversity within these species and for subsequent conservation purposes.

  7. Development and characterization of novel microsatellite loci for Lusitanian toadfish, Halobatrachus didactylus

    Directory of Open Access Journals (Sweden)

    Carla Sousa-Santos

    2015-01-01

    Full Text Available The Lusitanian toadfish Halobatrachus didactylus is an eastern Atlantic polygynous species showing male paternal care. In this paper we describe 5 novel microsatellite loci obtained by 454 GS-FLX Titanium pyrosequencing of a microsatellite-enriched library. The number of alleles per polymorphic locus varied between 2 and 4, and the observed heterozygosity ranged from 0.082 to 0.600. No significant deviation from Hardy–Weinberg equilibrium was found and there was no evidence for linkage disequilibrium. These markers will be of great value for paternity studies and population genetics of this species.

  8. DNA Slippage Occurs at Microsatellite Loci without Minimal Threshold Length in Humans: A Comparative Genomic Approach

    Science.gov (United States)

    Leclercq, Sébastien; Rivals, Eric; Jarne, Philippe

    2010-01-01

    The dynamics of microsatellite, or short tandem repeats (STRs), is well documented for long, polymorphic loci, but much less is known for shorter ones. For example, the issue of a minimum threshold length for DNA slippage remains contentious. Model-fitting methods have generally concluded that slippage only occurs over a threshold length of about eight nucleotides, in contradiction with some direct observations of tandem duplications at shorter repeated sites. Using a comparative analysis of the human and chimpanzee genomes, we examined the mutation patterns at microsatellite loci with lengths as short as one period plus one nucleotide. We found that the rates of tandem insertions and deletions at microsatellite loci strongly deviated from background rates in other parts of the human genome and followed an exponential increase with STR size. More importantly, we detected no lower threshold length for slippage. The rate of tandem duplications at unrepeated sites was higher than expected from random insertions, providing evidence for genome-wide action of indel slippage (an alternative mechanism generating tandem repeats). The rate of point mutations adjacent to STRs did not differ from that estimated elsewhere in the genome, except around dinucleotide loci. Our results suggest that the emergence of STR depends on DNA slippage, indel slippage, and point mutations. We also found that the dynamics of tandem insertions and deletions differed in both rates and size at which these mutations take place. We discuss these results in both evolutionary and mechanistic terms. PMID:20624737

  9. Characterization of microsatellite loci in the SLA class I region.

    Science.gov (United States)

    Chung, Hoyoung; McClure, Matthew Charles

    2011-04-01

    Microsatellite (MS) markers in the SLA-1 region were characterized via sequencing analysis with BAC clones generated from the National Institute of Health miniature pigs (MIPs). A total of 16 BAC clones were sequenced producing 15,228 shotgun reads, corresponding to 11.2 X sequencing coverage, that were used to construct a contig of 12.18 Mb in length. MS markers were compared with previously deposited GenBank sequences to verify the existence of 423 potential MS candidate markers in the SLA-1 region. Evaluation of these polymorphisms confirmed 59 markers in MIPs, and the combined data including sequences from GenBank revealed 155 polymorphic MS markers. MS markers identified from this analysis can be used to provide an alternative method to direct typing for determining an individual's SLA-1 haplotype. Copyright © 2010 Elsevier Inc. All rights reserved.

  10. Microsatellite loci in Japanese quail and cross-species amplification in chicken and guinea fowl

    Directory of Open Access Journals (Sweden)

    Mizutani Makoto

    2002-03-01

    Full Text Available Abstract In line with the Gifu University's initiative to map the Japanese quail genome, a total of 100 Japanese quail microsatellite markers isolated in our laboratory were evaluated in a population of 20 unrelated quails randomly sampled from a colony of wild quail origin. Ninety-eight markers were polymorphic with an average of 3.7 alleles per locus and a mean heterozygosity of 0.423. To determine the utility of these markers for comparative genome mapping in Phasianidae, cross-species amplification of all the markers was tested with chicken and guinea fowl DNA. Amplification products similar in size to the orthologous loci in quail were observed in 42 loci in chicken and 20 loci in guinea fowl. Of the cross-reactive markers, 57.1% in chicken and 55.0% in guinea fowl were polymorphic when tested in 20 birds from their respective populations. Five of 15 markers that could cross-amplify Japanese quail, chicken, and guinea fowl DNA were polymorphic in all three species. Amplification of orthologous loci was confirmed by sequencing 10 loci each from chicken and guinea fowl and comparing with them the corresponding quail sequence. The microsatellite markers reported would serve as a useful resource base for genetic mapping in quail and comparative mapping in Phasianidae.

  11. Development and Characterization of Polymorphic Microsatellite Loci in Phellodendron amurense (Rutaceae

    Directory of Open Access Journals (Sweden)

    Jing-Hua Yu

    2013-03-01

    Full Text Available Premise of the study: Microsatellite markers were developed for the rare species Phellodendron amurense to assess the genetic diversity and population structure of this plant. Methods and Results: In total, 27 microsatellite markers were developed for P. amurense by using an enriched genomic library and hybridization; all of these primers successfully amplified DNA fragments in P. amurense. These markers were screened in 74 individuals from four populations in China; 15 loci were found to be polymorphic, with the number of alleles per locus ranging from one to nine. Conclusions: The microsatellite markers developed here represent a useful tool for studying the population genetic structure of P. amurense and to inform toward the development of effective conservation programs for this species.

  12. Development of the First Chloroplast Microsatellite Loci in Ginkgo biloba (Ginkgoaceae

    Directory of Open Access Journals (Sweden)

    Chun-Xiang Xie

    2013-07-01

    Full Text Available Premise of the study: To investigate population genetics, phylogeography, and cultivar origin of Ginkgo biloba, chloroplast microsatellite primers were developed. Methods and Results: Twenty-one chloroplast microsatellite markers were identified referring to the two published chloroplast genomes of G. biloba. Polymorphisms were assessed on four natural populations from the two refugia in China. Eight loci were detected to be polymorphic in these populations. The number of alleles per locus ranged from three to seven, and the unbiased haploid diversity per locus varied from 0.441 to 0.807. Conclusions: For the first time, we developed 21 chloroplast microsatellite markers for G. biloba, including 13 monomorphic and eight polymorphic ones within the assessed natural populations. These markers should provide a powerful tool for the study of genetic variation of both natural and cultivated populations of G. biloba, as well as cultivars.

  13. Isolation and Characterization of Sixteen Polymorphic Microsatellite Loci in the Golden Apple Snail Pomacea canaliculata

    Directory of Open Access Journals (Sweden)

    Yan Liu

    2011-09-01

    Full Text Available We report the characterization of 16 polymorphic microsatellite markers in the golden apple snail, Pomacea canaliculata, a pest registered in the list of “100 of the world’s worst invasive alien species”. The fast isolation by AFLP (Amplified Fragment Length Polymorphism of sequences containing repeats (FIASCO method was used to isolate microsatellite loci, and polymorphism was explored with 29 individuals collected in an invasive region from China. These primers showed a number of alleles per locus ranging from three to 13. The ranges of observed and expected heterozygosity were 0.310–0.966 and 0.523–0.898, respectively. These microsatellite markers described here will be useful for population genetic studies of P. canaliculata.

  14. Isolation and Characterization of Polymorphic Microsatellite Loci in Spondias radlkoferi (Anacardiaceae

    Directory of Open Access Journals (Sweden)

    Esther Aguilar-Barajas

    2014-11-01

    Full Text Available Premise of the study: Microsatellite markers were developed for Spondias radlkoferi to assess the impact of primate seed dispersal on the genetic diversity and structure of this important tree species of Anacardiaceae. Methods and Results: Fourteen polymorphic loci were isolated from S. radlkoferi through 454 GS-FLX Titanium pyrosequencing of genomic DNA. The number of alleles ranged from three to 12. The observed and expected heterozygosities ranged from 0.382 to 1.00 and from 0.353 to 0.733, respectively. The amplification was also successful in S. mombin and two genera of Anacardiaceae: Rhus aromatica and Toxicodendron radicans. Conclusions: These microsatellite loci will be useful to assess the genetic diversity and population structure of S. radlkoferi and related species, and will allow us to investigate the effects of seed dispersal by spider monkeys (Ateles geoffroyi on the genetic structure and diversity of S. radlkoferi populations in a fragmented rainforest.

  15. Isolation and characterization of microsatellite loci for Bixa orellana, an important source of natural dyes.

    Science.gov (United States)

    Dequigiovanni, G; Ramos, S L F; Zucchi, M I; Bajay, M M; Pinheiro, J B; Fabri, E G; Bressan, E A; Veasey, E A

    2014-10-31

    Annatto (Bixa orellana) is a plant native from the American continental tropical zone. The seeds are used to produce a carotenoid-based yellow to orange food coloring. Microsatellite markers were developed for the Brazilian native species Bixa orellana to describe its genetic diversity and structure as well as to support conservation studies. Twenty-five microsatellite loci were isolated and characterized using an enriched genomic library. Ten loci were polymorphic in the 50 accessions sampled in this study, while 15 were considered monomorphic. The mean number of alleles per locus was 3.8, ranging from 2 to 6 alleles per locus. Mean values for the observed and expected heterozygosities were 0.541 (ranging from 0 to 0.658) and 0.639 (ranging from 0.422 to 0.787), respectively. All markers described in this study will be useful in further studies evaluating the genetic diversity, population dynamics, and conservation genetics of Bixa orellana.

  16. Isolation and Characterization of Microsatellite Loci for a Bioenergy Grass, Miscanthus sacchariflorus (Poaceae

    Directory of Open Access Journals (Sweden)

    Hai-Fei Zhou

    2013-01-01

    Full Text Available Premise of the study: Microsatellite loci were developed for the biomass C4 grass, Miscanthus sacchariflorus, and proved to be suitable markers for population genetic studies and germplasm management of this species. Methods and Results: Twenty-three polymorphic microsatellite loci were identified from an enriched genomic library of M. sacchariflorus. The polymorphism was assessed in 50 individuals from two populations in China. The number of alleles per locus varied from two to 18, with a mean of 8.13. The observed and expected heterozygosities ranged from 0.2 to 1.0 and from 0.198 to 0.898, respectively. Conclusions: These new markers will be useful for further investigation of genetic diversity and population genetic structure as well as molecular breeding of Miscanthus species.

  17. Characterization of Microsatellite Loci in the Lichen Fungus Lobaria pulmonaria (Lobariaceae

    Directory of Open Access Journals (Sweden)

    Silke Werth

    2013-02-01

    Full Text Available Premise of the study: Microsatellite loci were developed for the threatened haploid lichen fungus Lobaria pulmonaria to increase the resolution to identify clonal individuals, and to study its population subdivision. Methods and Results: We developed 14 microsatellite markers from 454 DNA sequencing data of L. pulmonaria and tested for cross-amplification with L. immixta and L. macaronesica. The number of alleles per locus ranged from two to 23. Nei's unbiased gene diversity, averaged over loci, ranged from 0.434 to 0.517 in the three studied populations. Conclusions: The new markers will increase the genetic resolution in studies that aim at disentangling clones in L. pulmonaria and may be useful for closely related species within Lobaria sect. Lobaria.

  18. Development of new VNTR markers for pike and assessment of variability at di- and tetranucleotide repeat microsatellite loci

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Taggart, J.B.; Meldrup, Dorte

    1999-01-01

    -0.57), though one highly variable microsatellite (13 alleles; expected heterozygosity 0.79) was identified. In combination with previously published microsatellites a set consisting of nine polymorphic loci appeared to be useful for discriminating populations, as determined by assignment tests. (C) 1999...

  19. Genetic Diversity of Three Spotted Seahorse, Hippocampus trimaculatus (Leach, 1814 in India Using Four Microsatellite Loci

    Directory of Open Access Journals (Sweden)

    Muthusamy THANGARAJ

    2012-11-01

    Full Text Available Seahorse populations are declining year by year not only in India but also throughout the world, because of over-fishing and increasing demand in Chinese market. The three spotted seahorse, Hippocampus trimaculatus is one of the dominant species and distributed all along the Indian coast. To study the genetic structure is very essential to conserve these species effectively. Hippocampus trimaculatus samples (n = 60/population were collected from Mullimunai in Palk Bay, Tuticorin in Gulf of Mannar and Vizhinjam in south Malabar in India as by-catch in small trawlnets. Microsatellites are being widely applied in animal genome mapping and phylogenetic analysis because of their co-dominant inheritance and high degree of polymorphism. The molecular polymorphism of microsatellite DNA has proved to be a potent tool in the analysis of several aspects of population genetics. In the present study, four microsatellite primers were used to investigate the genetic difference and structure of three selected populations of H. trimaculatus. The result showed the overall FST value (0.0989 of the microsatellite loci between Mullimunai and Vizhinjam was significantly different. The genetic distance between Mullimunai and Tuticorin was 0.183; between Tuticorin and Vizhinjam was 0.461; and Mullimunai and Vizhinjam was 0.837. There was no statistical evidence of recent severe bottlenecks in any of the three populations. Continuous monitoring of microsatellite variations within the populations of all the three locations was suggested to determine whether genetic variation within the populations is stabilized between year classes.

  20. Microsatellite loci in the tiger shark and cross-species amplification using pyrosequencing technology

    Science.gov (United States)

    Mendes, Natália J.; Cruz, Vanessa P.; Ashikaga, Fernando Y.; Camargo, Sâmia M.; Oliveira, Claudio; Piercy, Andrew N.; Burgess, George H.; Coelho, Rui; Santos, Miguel N.; Foresti, Fausto

    2016-01-01

    The tiger shark (Galeocerdo cuvier) has a global distribution in tropical and warm temperate seas, and it is caught in numerous fisheries worldwide, mainly as bycatch. It is currently assessed as near threatened by the International Union for Conservation of Nature (IUCN) Red List. In this study, we identified nine microsatellite loci through next generation sequencing (454 pyrosequencing) using 29 samples from the western Atlantic. The genetic diversity of these loci were assessed and revealed a total of 48 alleles ranging from 3 to 7 alleles per locus (average of 5.3 alleles). Cross-species amplification was successful at most loci for other species such as Carcharhinus longimanus, C. acronotus and Alopias superciliosus. Given the potential applicability of genetic markers for biological conservation, these data may contribute to the population assessment of this and other species of sharks worldwide. PMID:27635306

  1. Polymorphic Microsatellite Loci for Virola sebifera (Myristicaceae Derived from Shotgun 454 Pyrosequencing

    Directory of Open Access Journals (Sweden)

    Na Wei

    2013-04-01

    Full Text Available Premise of the study: Polymorphic microsatellite loci were characterized in the dioecious neotropical rainforest tree Virola sebifera. The markers will be used to study ecological and genetic impacts of hunting and landscape change in this vertebrate-dispersed, insect-pollinated tree species. Methods and Results: Simple sequence repeat (SSR markers were screened from genomic libraries of South American V. sebifera obtained by shotgun 454 pyrosequencing. Primer pairs were tested on Panamanian samples (N = 42. Approximately 52% of the 61 tested SSR markers amplified, and 16% were polymorphic. Ten selected polymorphic SSR loci contained seven to 15 alleles per locus, and polymorphic information content averaged 0.694. Observed heterozygosity ranged from 0.465 to 0.905, and expected heterozygosity was between 0.477 and 0.876. Conclusions: The 10 polymorphic loci will be useful in studying gene flow and genetic structure at local and regional spatial scales in V. sebifera.

  2. Development of 22 new microsatellite loci for fishers (Martes pennanti) with variability results from across their range

    NARCIS (Netherlands)

    Jordan, Mark J.; Higley, Mark; Matthews, Sean M.; Rhodes, Olin E.; Schwartz, Michael K.; Barrett, Reginald H.; Palsboll, Per J.

    2007-01-01

    We developed 22 new microsatellite loci for the fisher (Martes pennanti), a North American mesocarnivore. The loci were developed with samples from the southern Sierra Nevada Mountains in California, and were screened with samples from this population and four other populations. We observed a range

  3. Genetic variation in BoLA microsatellite loci in Portuguese cattle breeds.

    Science.gov (United States)

    Bastos-Silveira, C; Luís, C; Ginja, C; Gama, L T; Oom, M M

    2009-02-01

    Major histocompatibility complex (MHC) typing based on microsatellites can be a valuable approach to understanding the selective processes occurring at linked or physically close MHC genes and can provide important information on variability and relationships of populations. Using microsatellites within or in close proximity with bovine lymphocyte antigen (BoLA) genes, we investigated the polymorphisms in the bovine MHC, known as the BoLA, in eight Portuguese cattle breeds. Additional data from non-BoLA microsatellite loci were also used to compare the variability between these regions. Diversity was higher in BoLA than in non-BoLA microsatellites, as could be observed by the number of alleles, allelic richness and observed heterozygosity. Brava de Lide, a breed selected for aggressiveness and nobility, presented the lowest values of observed heterozygosity and allelic richness in both markers. Results from neutrality tests showed few statistically significant differences between the observed Hardy-Weinberg homozygosity (F) and the expected homozygosity (F(E)), indicating the apparent neutrality of the BoLA microsatellites within the analysed breeds. Nevertheless, we detected a trend of lower values of observed homozygosity compared with the expected one. We also detected some differences in the levels of allelic variability among the four BoLA microsatellites. Our data showed a higher number of alleles at the BoLA-DRB3 locus than at the BoLA-DRBP1 locus. These differences could be related to their physical position in the chromosome and may reflect functional requirements for diversity.

  4. Isolation and characterization of microsatellite loci in Sisyrinchium (Iridaceae) and cross amplification in other genera.

    Science.gov (United States)

    Miz, R B; Tacuatiá, L O; Cidade, F W; de Souza, A P; Bered, F; Eggers, L; de Souza-Chies, T T

    2016-09-16

    Recent phylogenetic studies on Sisyrinchium strongly suggest that species classified in section Hydastylus and section Viperella belong to a single group of plants in recent adaptive radiation (Clade IV). These species neither present clear morphological differentiation among them nor show clear identification using DNA barcode markers. Thus, the main goal of this study was to develop a set of polymorphic microsatellite markers compatible for representative species of both sections to ensure variability that could be revealed by SSR markers. Therefore, microsatellite primers were isolated and characterized for Sisyrinchium palmifolium and S. marchioides. In addition, transferability of the developed primers was tested in Iridoideae, primarily in closely related species of Sisyrinchium. Sixteen microsatellite loci were developed from enriched genomic libraries, of which ten were polymorphic. GST values indicated higher differentiation among subpopulations of S. palmifolium than those from S. marchioides. Major transferability was obtained using primers isolated from S. marchioides. All primers exhibited higher rates of cross-amplification for species belonging to Clade IV of Sisyrinchium, as well as to the genera Calydorea and Herbertia. These developed microsatellite markers can be used as an efficient tool for characterization of genetic variability in species belonging to Iridoideae, as well as for studies on population dynamics, genetic structure, and mating system in other Sisyrinchium species.

  5. Development of polymorphic microsatellite loci for conservation genetic studies of the coral reef fish Centropyge bicolor.

    Science.gov (United States)

    Herrera, M; Saenz-Agudelo, P; Nanninga, G B; Berumen, M L

    2015-09-01

    A total of 23 novel polymorphic microsatellite marker loci were developed for the angelfish Centropyge bicolor through 454 sequencing, and further tested on two spatially separated populations (90 individuals each) from Kimbe Bay in Papua New Guinea. The mean ± s.e. number of alleles per locus was 14·65 ± 1·05, and mean ± s.e. observed (HO ) and expected (HE ) heterozygosity frequencies were 0·676 ± 0·021 and 0·749 ± 0·018, respectively. The markers reported here constitute the first specific set for this genus and will be useful for future conservation genetic studies in the Indo-Pacific region.

  6. Identification of seventeen microsatellite loci for conservation genetic studies of the endemic wrasse Coris bulbifrons

    KAUST Repository

    Van Der Meer, Martin H.

    2012-11-08

    Coral reefs around the world are in decline, in part due to various anthropogenic factors, including fishing pressure. Coris bulbifrons is a large wrasse endemic to only four oceanic locations off Australia\\'s east coast: Middleton Reef, Elizabeth Reef, Lord Howe Island and Norfolk Island. The species is listed as vulnerable by the IUCN due to the potential threat of overfishing. Although these remote locations, some within Marine protected Areas, experience limited fishing pressure, populations may quickly decline with minimal fishing effort as seen in the overfishing of other large wrasses. We developed primers for 17 microsatellite loci to examine gene flow, population genetic structure, and genetic diversity within and among these four locations. Observed heterozygosities ranged 0. 126-0. 752 in 37 individuals from Lord Howe Island indicating that these loci will be useful in C. bulbifrons population genetic studies. © 2012 Springer Science+Business Media Dordrecht.

  7. Characterization of Microsatellite Loci in Lichen-Forming Fungi of Bryoria Section Implexae (Parmeliaceae

    Directory of Open Access Journals (Sweden)

    Olga Nadyeina

    2014-07-01

    Full Text Available Premise of the study: The locally rare, haploid, lichen-forming fungi Bryoria capillaris, B. fuscescens, and B. implexa are associated with boreal forests and belong to Bryoria sect. Implexae. Recent phylogenetic studies consider them to be conspecific. Microsatellite loci were developed to study population structure in Bryoria sect. Implexae and its response to ecosystem disturbances. Methods and Results: We developed 18 polymorphic microsatellite markers using 454 pyrosequencing data assessed in 82 individuals. The number of alleles per locus ranged from two to 13 with an average of 4.6. Nei's unbiased gene diversity, averaged over loci, ranged from 0.38 to 0.52. The markers amplified with all three species, except for markers Bi05, Bi15, and Bi18. Conclusions: The new markers will allow the study of population subdivision, levels of gene introgression, and levels of clonal spread of Bryoria sect. Implexae. They will also facilitate an understanding of the effects of forest disturbance on genetic diversity of these lichen species.

  8. Development and characterization of microsatellite loci for the Neotropical orchid Trichocentrum pumilum

    Directory of Open Access Journals (Sweden)

    Lia Maris Orth Ritter Antiqueira

    2016-11-01

    Full Text Available Studies of genetic diversity and structure are key elements in designing effective in situ and ex situ management plans, especially for species experiencing forest fragmentation. To investigate the level of genetic diversity in populations of Trichocentrum pumilum, eight polymorphic microsatellite loci were developed and used for genotyping 96 specimens from four disturbed populations. Low genetic diversity within populations was found (average number of alleles per locus ranging from 3.75 to 4.25, observed and expected heterozygosities from 0.238 to 0.333 and from 0.450 to 0.482, respectively. The fixation index (FIS ranged from 0.35 to 0.47, with significant values for all populations. No genotypic disequilibrium was detected. A mixed breeding system was found through an apparent outcrossing rate estimate. Our results suggest that these microsatellite loci are suitable for genetic studies of this species, showing low within population genetic diversity and moderate structure for T. pumilum populations.

  9. Characterization of Microsatellite Loci in the Himalayan Lichen Fungus Lobaria pindarensis (Lobariaceae

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    Shiva Devkota

    2014-04-01

    Full Text Available Premise of the study: Microsatellite loci were developed for the rare, Himalayan, endemic haploid lichen fungus, Lobaria pindarensis, to study its population subdivision and the species' response to forest disturbance and fragmentation. Methods and Results: We developed 18 polymorphic microsatellite markers using 454 pyrosequencing data and assessed them in 109 individuals. The number of alleles per locus ranged from three to 11 with an average of 6.9. Nei's unbiased gene diversity, averaged over loci, ranged from 0.514 to 0.685 in the three populations studied. The cross-amplification success with related species (L. chinensis, L. gyrophorica, L. isidiophora, L. orientalis, L. pulmonaria, L. spathulata, and Lobaria sp. was generally high and decreased with decreasing relationship to L. pindarensis. Conclusions: The new markers will allow the study of genetic diversity and differentiation within L. pindarensis across its distribution. Moreover, they will enable us to study the effects of forest management on the genetic population structure of this tree-colonizing lichen and to carry out population genetic studies of related species in East Asia.

  10. Isolation of 18 Microsatellite Loci in the Desert Mistletoe Phoradendron californicum (Santalaceae Via 454 Pyrosequencing

    Directory of Open Access Journals (Sweden)

    Juan M. Arroyo

    2013-12-01

    Full Text Available Premise of the study: Microsatellite primers were developed for the parasitic mistletoe Phoradendron californicum to investigate to what extent population genetic structure depends on host tree distribution within a highly fragmented landscape. Methods and Results: Fourteen unlinked polymorphic and four monomorphic nuclear microsatellite markers were developed using a genomic shotgun pyrosequencing method. A total of 187 alleles plus four monomorphic loci alleles were found in 98 individuals sampled in three populations from the Sonoran Desert in the Baja California peninsula (Mexico. Loci averaged 13.3 alleles per locus (range 4–28, and observed and expected heterozygosities within populations varied from 0.167–0.879 and 0.364–0.932, respectively. Conclusions: Levels of polymorphism of the reported markers are adequate for studies of diversity and fragmentation in natural populations of this parasitic plant. Cross-species amplifications in P. juniperinum and P. diguetianum only showed four markers that could be useful in P. diguetianum.

  11. Cytogenetics and characterization of microsatellite loci for a South American pioneer tree species, Croton floribundus.

    Science.gov (United States)

    Silvestrini, Milene; Pinto-Maglio, Cecília A F; Zucchi, Maria I; dos Santos, Flavio A M

    2013-12-01

    Despite the recent advances in plant population genetic studies, the lack of information regarding pedigree, ploidy level, or mode of inheritance for many polyploids can compromise the analysis of the molecular data produced. The aim of this study was to examine both microsatellite and cytogenetic characteristics of the pioneer tree Croton floribundus Spreng. (Euphorbiaceae) to test for the occurrence of polyploidy in the species and to evaluate its implications for the appropriate use of SSR markers. Seven microsatellite markers were developed and screened for 62 individuals from a semi-deciduous tropical forest in Brazil. Chromosome number, meiotic behavior, and pollen viability were evaluated from male flower buds. All SSR loci were highly polymorphic. The number of bivalents observed in meiosis n = 56 (2n = 8× = 112) and the maximum number of alleles per individual (Ni = 8) demonstrated the occurrence of polyploidy in C. floribundus. The normal meiotic pairing and the high pollen viability suggested that C. floribundus is a regular and stable polyploid, most likely an allopolyploid. The combined SSR and cytogenetic data provided new evidence on the origin and evolution of the species as well as assured the accurate use of SSR loci for population genetic studies of the polyploid pioneer species.

  12. Isolation and Characterization of Microsatellite Loci in Byrsonima cydoniifolia (Malpighiaceae and Cross-Amplification in B. crassifolia

    Directory of Open Access Journals (Sweden)

    Vanessa Bernardes

    2014-05-01

    Full Text Available Premise of the study: Microsatellite markers were developed and characterized in Byrsonima cydoniifolia (Malpighiaceae to allow further investigation of genetic variation in natural populations. Cross-amplification was tested in the related species B. crassifolia. Methods and Results: Seventeen microsatellite markers were isolated by a microsatellite-enriched library protocol. Fourteen polymorphic and three monomorphic loci were identified in B. cydoniifolia. The mean number of alleles in the three populations were 6.5, 6.5, and 8.2, ranging from three to 17 for different loci and populations. Mean observed and expected heterozygosities were 0.706 and 0.727, respectively. The fixation index was close to zero for all but two loci. Nine microsatellite loci were successfully cross-amplified in B. crassifolia. Conclusions: This new set of microsatellite markers will be a useful tool for genetic studies of B. cydoniifolia, supporting strategies for maintaining the genetic diversity of this species and possibly that of many related species.

  13. Mutations of microsatellite autosomal loci in paternity investigations of the Southern Poland population.

    Science.gov (United States)

    Wojtas, Marta; Piniewska, Danuta; Polańska, Nina; Stawowiak, Agnieszka; Sanak, Marek

    2013-05-01

    In this study, germline mutations were analyzed for 26,040 parent-child allelic transfers among subjects referred to paternity testing and originating from the Slavonic population of the Southern Poland. Mutation rates were estimated for 15 autosomal microsatellite loci: D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA. There were 35 mutation events observed at 11 from 15 analyzed loci. No mutations were found at TH01, D2S1338, D19S433 and TPOX loci. The mutation rate estimate was 0.0019 [0.0012-0.0028 95% CI] for paternal and 0.0004 [0.0002-0.0009] for maternal meiosis, while 25% mutations remained unassigned. The locus-specific mutation rate ranged from 0.0000 [0.0000-0.0014] to 0.0046 [0.0022-0.0087]. Mutations observed in male germlines were more frequent than in female germlines.

  14. Development and Characterization of Microsatellite Loci for the Moroccan Endemic Endangered Species Argania spinosa (Sapotaceae

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    Yasmina El Bahloul

    2014-03-01

    Full Text Available Premise of the study: Microsatellite loci were developed for the Moroccan endemic endangered species Argania spinosa with a combination of a typical library enrichment procedure and a 454 GS FLX Titanium–based high-throughput sequencing approach. Methods and Results: A genomic DNA library was enriched and further screened using (GA15, (GTA8, and (TTC8 biotin-labeled probes coupled with chemi-luminescence detection. To increase simple sequence repeat (SSR loci number, an ultra-high-throughput sequencing-based approach was used. Evaluation of all primer pairs was performed with labeled dUTP on an ABI 3130xl sequencer. Eleven polymorphic SSR loci were selected out of 79 SSR regions and extensively characterized on 150 individuals from eight populations. Total alleles ranged from six to 19 alleles per locus while expected heterozygosity ranged from 0.618 to 0.869. Conclusions: The SSRs developed here will be used to further characterize the genetic diversity of A. spinosa across its distribution range, mainly in the southern part of Morocco and southwestern Algeria. They may also be transferable to other Sapotaceae species.

  15. Development and characterization of microsatellite loci for the Moroccan endemic endangered species Argania spinosa (Sapotaceae).

    Science.gov (United States)

    El Bahloul, Yasmina; Dauchot, Nicolas; Machtoun, Ikrame; Gaboun, Fatima; Van Cutsem, Pierre

    2014-04-01

    Microsatellite loci were developed for the Moroccan endemic endangered species Argania spinosa with a combination of a typical library enrichment procedure and a 454 GS FLX Titanium-based high-throughput sequencing approach. • A genomic DNA library was enriched and further screened using (GA)15, (GTA)8, and (TTC)8 biotin-labeled probes coupled with chemi-luminescence detection. To increase simple sequence repeat (SSR) loci number, an ultra-high-throughput sequencing-based approach was used. Evaluation of all primer pairs was performed with labeled dUTP on an ABI 3130xl sequencer. Eleven polymorphic SSR loci were selected out of 79 SSR regions and extensively characterized on 150 individuals from eight populations. Total alleles ranged from six to 19 alleles per locus while expected heterozygosity ranged from 0.618 to 0.869. • The SSRs developed here will be used to further characterize the genetic diversity of A. spinosa across its distribution range, mainly in the southern part of Morocco and southwestern Algeria. They may also be transferable to other Sapotaceae species.

  16. Development and characterization of microsatellite loci for the Moroccan endemic endangered species Argania spinosa (Sapotaceae)1

    Science.gov (United States)

    El Bahloul, Yasmina; Dauchot, Nicolas; Machtoun, Ikrame; Gaboun, Fatima; Van Cutsem, Pierre

    2014-01-01

    • Premise of the study: Microsatellite loci were developed for the Moroccan endemic endangered species Argania spinosa with a combination of a typical library enrichment procedure and a 454 GS FLX Titanium–based high-throughput sequencing approach. • Methods and Results: A genomic DNA library was enriched and further screened using (GA)15, (GTA)8, and (TTC)8 biotin-labeled probes coupled with chemi-luminescence detection. To increase simple sequence repeat (SSR) loci number, an ultra-high-throughput sequencing-based approach was used. Evaluation of all primer pairs was performed with labeled dUTP on an ABI 3130xl sequencer. Eleven polymorphic SSR loci were selected out of 79 SSR regions and extensively characterized on 150 individuals from eight populations. Total alleles ranged from six to 19 alleles per locus while expected heterozygosity ranged from 0.618 to 0.869. • Conclusions: The SSRs developed here will be used to further characterize the genetic diversity of A. spinosa across its distribution range, mainly in the southern part of Morocco and southwestern Algeria. They may also be transferable to other Sapotaceae species. PMID:25202614

  17. Genotypic characterization of ten microsatellite loci in two Brazilian free range (Caipira chicken lines

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    Mari Helen Pagani Possamai

    2015-05-01

    Full Text Available This study aimed to investigate the genetic variability of two Brazilian free range (Caipira chickens lines using microsatellites analysis of ten loci. It was collected a total of 99 blood samples, which 49 were from Paraíso Pedrês (PP and 50 were from Rubro Negra (RN lines. The amplification of the DNA fragments was performed by polymerase chain reaction (PCR and the genotyping was conduct using ABI 3130 sequencer. The allele number variation was among 3 (LEI0254 to 32 (LEI0212 in the PP line, and 4 (LEI0254 to 31 (LEI0212 in the RN line. The allelic average per locus was 13.3 and 13.1 in the PP and RN lines, respectively. The average observed and the expected heterozygosity were 0.650 and 0.820 in the PP line, and 0.671 and 0.804 in the RN line. All of the analyzed loci were informative (PIC>0.5. These results indicate that these free-range animals have a high genetic variability, at least for the majority of the analyzed loci, and this genetic variation is higher than the commercial chickens and similar for the no-commercial birds

  18. Development of Microsatellite Loci for Cyclocarya paliurus (Juglandaceae, A Monotypic Species in Subtropical China

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    Deng-Mei Fan

    2013-06-01

    Full Text Available Premise of the study: Microsatellite loci were developed for a monotypic species endemic to subtropical China, Cyclocarya paliurus, to help infer the evolutionary histories of ancient monotypic genera in subtropical China. Methods and Results: Using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO protocol, 28 primer sets were identified in two wild populations. All loci were polymorphic, with the number of alleles per locus ranging from two to eight. The expected and observed heterozygosities ranged from 0.153 to 0.802 and from 0 to 0.750, respectively. The transferability of the 28 primer pairs was tested on Juglans regia, Pterocarya stenoptera, and Platycarya strobilacea. Twenty-one (75.0%, 22 (78.6%, and 15 (53.6% markers were successfully amplified in J. regia, P. stenoptera, and P. strobilacea, respectively. Conclusions: These loci will be useful for in-depth analysis of genetic diversity and phylogeographical variation throughout the distribution range of C. paliurus.

  19. Polymorphism of microsatellite loci in bread wheat (Triticum aestivum L. and related species

    Directory of Open Access Journals (Sweden)

    Kondić-Špika Ankica Đ.

    2016-01-01

    Full Text Available This study analysed polymorphism of 15 microsatellite loci in the col­lection comprising of 40 genotypes of bread wheat (Triticum aestivum L., 32 genotypes belonging to other species within Triticum genus and 3 genotypes from Aegilops genus. The results showed significant differences in the variability of the tested loci in bread wheat and related species. In the collection of bread wheat genotypes, 119 alleles were detected with the average number of 7.9 alleles per locus. In wild and cultivated related species 157 alleles were identified, with the average of 10.5 alleles per locus. All analysed parameters of micro­satellite loci variability (PIC value, gene diversity, heterozygosity, etc. indicated higher level of polymorphism in wild relatives than in the cultivated bread wheat. Analyses of individual genomes indicated that in the bread wheat genetic diversity of the B and D genomes was significantly reduced in relation to the A genome, while the differences in polymorphism between genomes in the wild relatives were significantly lower. The results showed that wild related species can be used as sources for new variability in wheat breeding. [Project of the Serbian Ministry of Education, Science and Technological Development

  20. Cloning and characterization of 29 tetranucleotide and two dinucleotide polymorphic microsatellite loci from the endangered marbled murrelet (Brachyramphus marmoratus)

    NARCIS (Netherlands)

    Rew, MB; Peery, MZ; Beissinger, Steven R.; Berube, M; Lozier, JD; Rubidge, EM; Palsboll, PJ

    2006-01-01

    We developed 31 novel, polymorphic microsatellite loci in the marbled murrelet (Brachyramphus marmoratus), a critically endangered seabird. Variability was tested on 15 individuals from the Santa Cruz, California population, with each locus characterized by two to 12 alleles. Observed levels of hete

  1. Inheritance mode of microsatellite loci and their use for kinship analysis in the Pacific oyster (Crassostrea gigas)

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Five full-sib families of the Pacific oyster (Crassostrea gigas) larvae were used to study the mode of inheritance at eight microsatellite loci, and the feasibility of these markers for kinship estimate was also examined. All eight microsatellite loci were compatible with Mendelian inheritance. Neither evidence of sex-linked barriers to transmission nor evidence of major barriers to fertilization between gametes from the parents was shown. Three of the eight loci showed the presence of null alleles in four families, demonstrating the need to conduct comprehensive species-specific inheritance studies for microsatellite loci used in population genetic studies. Although the null allele heterozygotes were considered as homozygotes in the calculation of genetic distance, offspring from five full-sib families were unambiguously discriminated in the neighbor-joining dendrogram. This result indicates that the microsatellite markers may be capable of discriminating between related and unrelated oyster larvae in the absence of pedigree information, and is applicable to the investigation of the effective number of parents contributing to the hatchery population of the Pacific oyster.

  2. Population structure of the African savannah elephant inferred from mitochondrial control region sequences and nuclear microsatellite loci

    DEFF Research Database (Denmark)

    Nyakaana, S; Arctander, P; Siegismund, H R

    2002-01-01

    Two hundred and thirty-six mitochondrial DNA nucleotide sequences were used in combination with polymorphism at four nuclear microsatellite loci to assess the amount and distribution of genetic variation within and between African savannah elephants. They were sampled from 11 localities in eastern...... populations and 44 alleles in the total sample were found. The gene diversity ranged from 0.51 to 0.72 in the localities studied. An analysis of molecular variance showed significant genetic differentiation between populations within regions and also between regions. The extent of subdivision between...... populations at the mtDNA control region was approximately twice as high as shown by the microsatellite loci (mtDNA F(ST) = 0.59; microsatellite R(ST) = 0.31). We discuss our results in the light of Pleistocene refugia and attribute the observed pattern to population divergence in allopatry accompanied...

  3. Development and characterization of 16 polymorphic microsatellite loci for the Alaska blackfish (Esociformes: Dallia pectoralis)

    Science.gov (United States)

    Campbell, Matthew A.; Sage, George K.; DeWilde, Rachel L.; López, J. Andres; Talbot, Sandra L.

    2014-01-01

    Blackfishes (Esociformes: Esocidae: Dallia), small fishes with relictual distributions, are unique in being the only primary freshwater fish genus endemic to Beringia. Although the number of species of Dallia is debated, disjunct populations and distinct mitochondrial divisions that predate the end of the last glacial maximum are apparent. We developed sixteen polymorphic microsatellites from the Alaska blackfish (Dallia pectoralis) to study genetic diversity in Dallia. Genotypes from two populations, Denali (n = 31) and Bethel (n = 35), demonstrated the usefulness of the loci for population-level investigation. Observed and expected heterozygosity averaged 18.6 and 19.8 % in Denali and 61.1 and 63.7 % in Bethel. Number of alleles at each locus averaged 3.50 in Denali and 9.63 in Bethel. The observed signature of variability and structuring between populations is consistent with mitochondrial data.

  4. Development of polymorphic microsatellite loci for conservation genetic studies of the coral reef fish Centropyge bicolor

    KAUST Repository

    Herrera, M.

    2015-08-14

    A total of 23 novel polymorphic microsatellite marker loci were developed for the angelfish Centropyge bicolor through 454 sequencing, and further tested on two spatially separated populations (90 individuals each) from Kimbe Bay in Papua New Guinea. The mean ± s.e. number of alleles per locus was 14·65 ± 1·05, and mean ± s.e. observed (HO) and expected (HE) heterozygosity frequencies were 0·676 ± 0·021 and 0·749 ± 0·018, respectively. The markers reported here constitute the first specific set for this genus and will be useful for future conservation genetic studies in the Indo-Pacific region. © 2015 The Fisheries Society of the British Isles.

  5. Characterization and cross-amplification of 13 microsatellite loci in the northern pine processionary moth, Thaumetopoea pinivora (Lepidoptera: Notodontidae).

    Science.gov (United States)

    Cassel-Lundhagen, Anna; Ronnås, Cecilia; Frauenfelder, Nathalie

    2009-05-01

    Thirteen polymorphic microsatellite loci were developed for the northern pine processionary moth (Thaumetopoea pinivora) and tested for cross-amplification in seven other species within the Thaumetopoea family. Number of alleles ranged from two to 10 when at least 28 individuals from one population were screened and one locus, Thapin06, appears to be sex linked. Expected heterozygosity ranged from 0.094 to 0.856 and observed heterozygosity ranged from 0.097 to 0.806. Amplification success varied between sister species, with two up to seven loci being successfully amplified. The described loci will be valuable for studying the population genetic structure and dispersal behaviour of this forest pest.

  6. Microsatellites loci reveal heterozygosis and population structure in vampire bats (Desmodus rotundus) (Chiroptera: Phyllostomidae) of Mexico.

    Science.gov (United States)

    Romero-Nava, Claudia; León-Paniagua, Livia; Ortega, Jorge

    2014-06-01

    A limited number of studies have focused on the population genetic structure of vampire bats (Desmous rotundus) in America. This medium-sized bat is distributed in tropical areas of the continent with high prevalence in forested livestock areas. The aim of this work was to characterize the vampire population structure and their genetic differentiation. For this, we followed standard methods by which live vampires (caught by mist-netting) and preserved material from scientific collections, were obtained for a total of 15 different locations, ranging from Chihuahua (North) to Quintana Roo (Southeast). Tissue samples were obtained from both live and collected animals, and the genetic differentiation, within and among localities, was assessed by the use of seven microsatellite loci. Our results showed that all loci were polymorphic and no private alleles were detected. High levels of heterozygosis were detected when the proportion of alleles in each locus were compared. Pairwise (ST) and R(ST) detected significant genetic differentiation among individuals from different localities. Our population structure results indicate the presence of eleven clusters, with a high percentage of assigned individuals to some specific collecting site.

  7. Microsatellites loci reveal heterozygosis and population structure in vampire bats (Desmodus rotundus (Chiroptera: Phyllostomidae of Mexico

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    Claudia Romero-Nava

    2014-08-01

    Full Text Available A limited number of studies have focused on the population genetic structure of vampire bats (Desmodus rotundus in America. This medium-sized bat is distributed in tropical areas of the continent with high prevalence in forested livestock areas. The aim of this work was to characterize the vampire population structure and their genetic differentiation. For this, we followed standard methods by which live vampires (caught by mist-netting and preserved material from scientific collections, were obtained for a total of 15 different locations, ranging from Chihuahua (North to Quintana Roo (Southeast. Tissue samples were obtained from both live and collected animals, and the genetic differentiation, within and among localities, was assessed by the use of seven microsatellite loci. Our results showed that all loci were polymorphic and no private alleles were detected. High levels of heterozygosis were detected when the proportion of alleles in each locus were compared. Pairwise F ST and R ST detected significant genetic differentiation among individuals from different localities. Our population structure results indicate the presence of eleven clusters, with a high percentage of assigned individuals to some specific collecting site. Rev. Biol. Trop. 62 (2: 659-669. Epub 2014 June 01.

  8. Molecular identification of Greek olive (Olea europaea) cultivars based on microsatellite loci.

    Science.gov (United States)

    Roubos, K; Moustakas, M; Aravanopoulos, F A

    2010-01-01

    Olea europaea is one of the oldest species of domesticated trees. We used microsatellite markers for fingerprinting and for evaluation of genetic similarity and structure of 26 Greek olive cultivars, which cover most of the olive cultivation regions of Greece, including previously undescribed denominations from northern Greece. Eighty-one alleles were revealed with six SSR loci that were selected as most informative of 10 SSR primers that were initially investigated. The number of alleles per locus varied from 7 to 20 (mean, 13.5). Heterozygosity ranged from 0.240 at locus DCA-3 to 0.826 at locus UDO99-9, with a mean value of 0.600. Analysis of 104 trees representing 26 denominations (four trees per denomination) revealed 26 distinct SSR profiles, indicating 26 olive cultivars; no intracultivar variability was observed. Genetic and geographic distances were not significantly correlated, based on the Mantel test. These SSR loci allowed unequivocal identification of all the cultivars and will be useful for future breeding and olive germplasm management efforts.

  9. Two sex-chromosome-linked microsatellite loci show geographic variance among North American Ostrinia nubilalis

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    Brad S. Coates

    2003-09-01

    Full Text Available PCR-based O. nubilalis population and pedigree analysis indicated female specificity of a (GAAAATn microsatellite, and male specificity of a CAYCARCGTCACTAA repeat unit marker. These loci were respectively named Ostrinia nubilalis W-chromosome 1 (ONW1 and O. nubilalis Z-chromosome 1 (ONZ1. Intact repeats of three, four, or five GAAAAT units are present among ONW1 alleles, and biallelic variation exists at the ONZ1 locus. Screening of 493 male at ONZ1 and 448 heterogametic females at ONZ1 and ONW1 loci from eleven North American sample sites was used to construct genotypic data. Analysis of molecular variance (AMOVA and F-statistics indicated no female haplotype or male ONZ1 allele frequency differentiation between voltinism ecotypes. Four subpopulations from northern latitudes, Minnesota and South Dakota, showed the absence of a single female haplotype, a significant deviation of ONZ1 data from Hardy-Weinberg expectation, and low-level geographic divergence from other subpopulations. Low ONZ1 and ONW1 allele diversity could be attributed either to large repeat unit sizes, low repeat number, reduced effective population (Ne size of sex chromosomes, or the result of recent O. nubilalis introduction and population expansion, but likely could not be due to inbreeding. These sequences have been deposited in GenBank AF442958, and AY102618 to AY102620.

  10. Isolation and characterization of microsatellite loci for alligator gar (Atractosteus spatula) and their variability in two other species (Lepisosteus oculatus and L. osseus) of Lepisosteidae

    Science.gov (United States)

    Moyer, G.R.; Sloss, Brian L.; Kreiser, B.R.; Feldheim, K.A.

    2009-01-01

    We report on the isolation of 17 polymorphic microsatellite loci from alligator gar (Atractosteus spatula), a large-bodied species that has experienced population declines across much of its range. These loci possessed 2-19 alleles and observed heterozygosities of 0-0.974. All loci conformed to Hardy-Weinberg equilibrium expectations, and none exhibited linkage disequilibrium. Nine and eight of these loci were found to be polymorphic in the related species Lepisosteus oculatus and L. osseus, respectively. These microsatellite loci should prove useful in conservation efforts of A. spatula through the study of population structure and hatchery broodstock management. ?? 2009 Blackwell Publishing Ltd.

  11. Development and characterization of sixteen microsatellite loci for Geosmithia morbida, the causal agent of thousand canker disease in black walnut (Juglans nigra)

    Science.gov (United States)

    Sixteen polymorphic microsatellite loci were identified from the fungal pathogen Geosmithia morbida. Loci were characterized for 13 different isolates collected in 2010 from symptomatic black walnut trees in Tennessee. A total of 77 loci were tested and 16 of those were optimized, screened and selec...

  12. Inheritance Pattern of Microsatellite Loci and Their Use for Kinship Analysis m the Japanese Scallop Patinopecten yessoensis

    Institute of Scientific and Technical Information of China (English)

    XU Kefeng; LI Qi

    2009-01-01

    The inheritance mode of seven microsatellite markers was investigated in Patinopecten yessoensis larvae from four con-trolled crosses, and the feasibility of using these markers for kinship estimation was also examined. All the seven microsatellite loci were compatible with Mendelian inheritance. Neither sex-linked barriers to transmission nor major barriers to fertilization between gametes from the parents were evident. Two of the seven loci showed the presence of null alleles in two families, suggesting the need to conduct comprehensive species-specific inheritance studies for microsatellite loci used in population genetic studies. However, even if the null allele heterozygotes were considered as homozygotes in the calculation of genetic distance, offspring from four fami-lies were all unambiguously discriminated in the neighbor-joining dendrogram. This result indicates that the microsatellite markers used may be capable of discriminating between related and unrelated scallop larvae in the absence of pedigree information, and of investigating the effective number of parents contributing to the hatchery population of the Japanese scallop.

  13. Isolation and Characterization of Eleven Polymorphic Microsatellite Loci for the Valuable Medicinal Plant Dendrobium huoshanense and Cross-Species Amplification

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    Hui Wang

    2012-12-01

    Full Text Available Dendrobium huoshanense (Orchidaceae is a perennial herb and a widely used medicinal plant in Traditional Chinese medicine (TCM endemic to Huoshan County town in Anhui province in Southeast China. A microsatellite-enriched genomic DNA library of D. huoshanense was developed and screened to identify marker loci. Eleven polymorphic loci were isolated and analyzed by screening 25 individuals collected from a natural population. The number of alleles per locus ranged from 2 to 5. The observed and expected heterozygosities ranged from 0.227 to 0.818 and from 0.317 to 0.757, respectively. Two loci showed significant deviations from Hardy-Weinberg equilibrium and four of the pairwise comparisons of loci revealed linkage disequilibrium (p < 0.05. These microsatellite loci were cross-amplified for five congeneric species and seven loci can be amplified in all species. These simple sequence repeats (SSR markers are useful in genetic studies of D. huoshanense and other related species and in conservation decision-making.

  14. Genomic conservation of cattle microsatellite loci in wild gaur (Bos gaurus and current genetic status of this species in Vietnam

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    Renard Jean-Paul

    2007-11-01

    Full Text Available Abstract Background The wild gaur (Bos gaurus is an endangered wild cattle species. In Vietnam, the total number of wild gaurs is estimated at a maximum of 500 individuals. Inbreeding and genetic drift are current relevant threats to this small population size. Therefore, information about the genetic status of the Vietnamese wild gaur population is essential to develop strategies for conservation and effective long-term management for this species. In the present study, we performed cross-species amplification of 130 bovine microsatellite markers, in order to evaluate the applicability and conservation of cattle microsatellite loci in the wild gaur genome. The genetic diversity of Vietnamese wild gaur was also investigated, based on data collected from the 117 successfully amplified loci. Results One hundred-thirty cattle microsatellite markers were tested on a panel of 11 animals. Efficient amplifications were observed for 117 markers (90% with a total of 264 alleles, and of these, 68 (58.1% gave polymorphic band patterns. The number of alleles per locus among the polymorphic markers ranged from two to six. Thirteen loci (BM1314, BM2304, BM6017, BMC2228, BMS332, BMS911, CSSM023, ETH123, HAUT14, HEL11, HEL5, ILSTS005 and INRA189 distributed on nine different cattle chromosomes failed to amplify wild gaur genomic DNA. Three cattle Y-chromosome specific microsatellite markers (INRA124, INRA126 and BM861 were also highly specific in wild gaur, only displaying an amplification product in the males. Genotype data collected from the 117 successfully amplified microsatellites were used to assess the genetic diversity of this species in Vietnam. Polymorphic Information Content (PIC values varied between 0.083 and 0.767 with a mean of 0.252 while observed heterozygosities (Ho ranged from 0.091 to 0.909 (mean of 0.269. Nei's unbiased mean heterozygosity and the mean allele number across loci were 0.298 and 2.2, respectively. Conclusion Extensive

  15. Short Communication Mendelian inheritance, linkage, and genotypic disequilibrium in microsatellite loci of Hymenaea stigonocarpa Mart. ex Hayne (Fabaceae-Caesalpinioideae).

    Science.gov (United States)

    Moraes, M A; Kubota, T Y K; Silva, E C B; Silva, A M; Cambuim, J; Moraes, M L T; Furlani Junior, E; Sebbenn, A M

    2016-07-29

    Hymenaea stigonocarpa is a deciduous and monoecious Neotropical tree species pollinated by bats. Due to overexploitation and habitat destruction, the population size has drastically diminished in nature. No previous study has investigated Mendelian inheritance, linkage, and genotypic disequilibrium in the available microsatellite markers in this species. So, our aim was to estimate these parameters using six microsatellite loci in a sample of 470 adults and 219 juveniles from two populations of H. stigonocarpa. In addition, 30 seeds per tree from 35 seed-trees were collected. Each seed was kept record of the seed-trees and fruit origin. Based on the six microsatellite loci, we found that only 10.6% of the cases showed significant deviations from Mendelian segregation and 15.3% showed linkage. We detected no evidence of genotypic disequilibrium between the loci in the adult trees or juveniles. Thus, our results suggest that these loci can be used with great accuracy in future genetic analyses of H. stigonocarpa populations.

  16. Cross-amplification and characterization of microsatellite loci in Acropora austera from the south-western Indian Ocean.

    Science.gov (United States)

    Montoya-Maya, P H; Macdonald, A H H; Schleyer, M H

    2014-02-27

    Here, we report the successful cross-species amplification of previously published acroporid microsatellite markers in the coral Acropora austera from the south-western Indian Ocean. This fast-growing species is a major reef-building coral on South African reefs; however, it is the most damaged coral by scuba diving activity, and is known to be very susceptible to coral bleaching. Neither genetic information nor symbiont-free host tissue was available to develop novel microsatellite markers for this species. Cross-species amplification of previously published microsatellite markers was considered as an alternative to overcome these problems. Of the 21 microsatellite markers tested, 6 were reliably amplified, scored, and found to contain polymorphic loci (3-15 alleles). Although microsatellite sequences are believed to be scarce in the Acropora genome because of its small size, the results of this study and previous research indicate that the microsatellite sequences are well conserved across Acropora species. A detailed screening process identified and quantified the sources of error and bias in the application of these markers (e.g., allele scoring error, failure rates, frequency of null alleles), and may be accounted for in the study of the contemporary gene flow of A. austera in the south-western Indian Ocean.

  17. Amplifiability of mitochondrial, microsatellite and amelogenin DNA loci from fecal samples of red brocket deer Mazama americana (Cetartiodactyla, Cervidae).

    Science.gov (United States)

    Oliveira, M L; Duarte, J M B

    2013-01-16

    We tried to amplify mitochondrial, microsatellite and amelogenin loci in DNA from fecal samples of a wild Mazama americana population. Fifty-two deer fecal samples were collected from a 600-ha seasonal semideciduous forest fragment in a subtropical region of Brazil (21°20'S, 47°17'W), with the help of a detection dog; then, stored in ethanol and georeferenced. Among these samples 16 were classified as "fresh" and 36 as "non-fresh". DNA was extracted using the QIAamp(®) DNA Stool Mini Kit. Mitochondrial loci were amplified in 49 of the 52 samples. Five microsatellite loci were amplified by PCR; success in amplification varied according to locus size and sample age. Successful amplifications were achieved in 10/16 of the fresh and in 13/36 of the non-fresh samples; a negative correlation (R = -0.82) was found between successful amplification and locus size. Amplification of the amelogenin locus was successful in 22 of the 52 samples. The difficulty of amplifying nuclear loci in DNA samples extracted from feces collected in the field was evident. Some methodological improvements, including collecting fresh samples, selecting primers for shorter loci and quantifying the extracted DNA by real-time PCR, are suggested to increase amplification success in future studies.

  18. Characterization of polymorphic microsatellite loci for two species of phyllostomid bats from the Greater Antilles (Erophylla sezekorni and Macrotus waterhousii).

    Science.gov (United States)

    Murray, Kevin L; Fleming, Theodore H; Gaines, Michael S; Williams, Dean A

    2008-05-01

    We developed 12 polymorphic microsatellite loci for the buffy flower bat (Erophylla sezekorni) and 10 loci for Waterhouse's big-eared bat (Macrotus waterhousii). In E. sezekorni, we tested 65 individuals from three islands, Cuba, Exuma, and Abaco. Mean number of alleles per locus was 10.7 (range 5-20). In M. waterhousii, we tested 39 individuals from one island, Exuma. Mean number of alleles per locus was 6.9 (range 4-13). We will use these markers to study the phylogeography and mating system of these species. © 2008 The Authors.

  19. Polymorphic microsatellite loci for the sand pocket mouse Chaetodipus arenarius, an endemic from the Baja California Peninsula

    Science.gov (United States)

    Munguia-Vega, A.; Rodriguez-Estrella, R.; Nachman, M.; Culver, M.

    2009-01-01

    Fifteen polymorphic microsatellite loci were isolated from an enriched genomic library of the sand pocket mouse Chaetodipus arenarius. The mean number of alleles per locus was 11.53 (range five to 19) and the average observed heterozygosity was 0.764 (range 0.121 to 1.0). The markers will be used for detecting the impact of human-induced habitat fragmentation on patterns of gene flow, genetic structure, and extinction risk. In addition, these markers will be useful across the genus because most of the loci cross-amplified and were polymorphic in three other species of Chaetodipus. ?? 2008 The Authors.

  20. Investigation of population structure in Gulf of Mexico Seepiophila jonesi (Polychaeta, Siboglinidae using cross-amplified microsatellite loci

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    Chunya Huang

    2016-08-01

    Full Text Available Background Vestimentiferan tubeworms are some of the most recognizable fauna found at deep-sea cold seeps, isolated environments where hydrocarbon rich fluids fuel biological communities. Several studies have investigated tubeworm population structure; however, much is still unknown about larval dispersal patterns at Gulf of Mexico (GoM seeps. As such, researchers have applied microsatellite markers as a measure for documenting the transport of vestimentiferan individuals. In the present study, we investigate the utility of microsatellites to be cross-amplified within the escarpiid clade of seep vestimentiferans, by determining if loci originally developed for Escarpia spp. could be amplified in the GoM seep tubeworm, Seepiophila jonesi. Additionally, we determine if cross-amplified loci can reliably uncover the same signatures of high gene flow seen in a previous investigation of S. jonesi. Methods Seventy-seven S. jonesi individuals were collected from eight seep sites across the upper Louisiana slope (<1,000 m in the GoM. Forty-eight microsatellite loci that were originally developed for Escarpia laminata (18 loci and Escarpia southwardae (30 loci were tested to determine if they were homologous and polymorphic in S. jonesi. Loci found to be both polymorphic and of high quality were used to test for significant population structuring in S. jonesi. Results Microsatellite pre-screening identified 13 (27% of the Escarpia loci were homologous and polymorphic in S. jonesi, revealing that microsatellites can be amplified within the escarpiid clade of vestimentiferans. Our findings uncovered low levels of heterozygosity and a lack of genetic differentiation amongst S. jonesi from various sites and regions, in line with previous investigations that employed species-specific polymorphic loci on S. jonesi individuals retrieved from both the same and different seep sites. The lack of genetic structure identified from these populations supports the

  1. Characterisation of 12 microsatellite loci in the Vietnamese commercial clam Lutraria rhynchaena Jonas 1844 (Heterodonta: Bivalvia: Mactridae) through next-generation sequencing.

    Science.gov (United States)

    Thai, Binh Thanh; Tan, Mun Hua; Lee, Yin Peng; Gan, Han Ming; Tran, Trang Thi; Austin, Christopher M

    2016-05-01

    The marine clam Lutraria rhynchaena is gaining popularity as an aquaculture species in Asia. Lutraria populations are present in the wild throughout Vietnam and several stocks have been established and translocated for breeding and aquaculture grow-out purposes. In this study, we demonstrate the feasibility of utilising Illumina next-generation sequencing technology to streamline the identification and genotyping of microsatellite loci from this clam species. Based on an initial partial genome scan, 48 microsatellite markers with similar melting temperatures were identified and characterised. The 12 most suitable polymorphic loci were then genotyped using 51 individuals from a population in Quang Ninh Province, North Vietnam. Genetic variation was low (mean number of alleles per locus = 2.6; mean expected heterozygosity = 0.41). Two loci showed significant deviation from Hardy-Weinberg equilibrium (HWE) and the presence of null alleles, but there was no evidence of linkage disequilibrium among loci. Three additional populations were screened (n = 7-36) to test the geographic utility of the 12 loci, which revealed 100 % successful genotyping in two populations from central Vietnam (Nha Trang). However, a second population from north Vietnam (Co To) could not be successfully genotyped and morphological evidence and mitochondrial variation suggests that this population represents a cryptic species of Lutraria. Comparisons of the Qang Ninh and Nha Trang populations, excluding the 2 loci out of HWE, revealed statistically significant allelic variation at 4 loci. We reported the first microsatellite loci set for the marine clam Lutraria rhynchaena and demonstrated its potential in differentiating clam populations. Additionally, a cryptic species population of Lutraria rhynchaena was identified during initial loci development, underscoring the overlooked diversity of marine clam species in Vietnam and the need to genetically characterise population representatives prior

  2. Genetic Diversity and Population Structure for the Conservation of Giant Spiny Frog (Quasipaa spinosa) Using Microsatellite Loci and Mitochondrial DNA

    Institute of Scientific and Technical Information of China (English)

    Danna YU; Rongquan ZHENG; Qinfang LU; Guang YANG; Yao FU; Yun ZHANG

    2016-01-01

    The giant spiny frog (Quasipaa spinosa) is an endangered species with a relatively small distribution limited to southern China and Northern Vietnam. This species is becoming increasingly threatened because of over-exploitation and habitat degradation. This study provides data on the genetic diversity and population genetic structure of the giant spiny frog to facilitate the further development of effective conservation recommendations for this economically important but threatened species. We examined 10 species-specific microsatellite loci and Cyt b genes (562 bp) collected from 13 wild populations across the entire range of this species. Results of 10 microsatellite loci analysis showed a generally high level of genetic diversity. Moreover, the genetic differentiation among all 12 populations was moderate to large (overall FST= 0.1057). A total of 51 haplotypes were identified for Cyt b, which suggests high haplotype nucleotide diversities. Phylogeographic and population structure analyses using both DNA markers suggested that the wild giant spiny frog can be divided into four distinct major clades, i.e., Northern Vietnam, Western China, Central China, and Eastern China. The clades with significant genetic divergence are reproductively isolated, as evidenced by a high number of private alleles and strong incidence of failed amplification in microsatellite loci. Our research, coupled with other studies, suggests that Q. spinosa might be a species complex within which no detectable morphological variation has been revealed. The four phylogenetic clades and some subclades with distinct geographical distribution should be regarded as independent management units for conservation purposes.

  3. Heterologous primer transferability and access to microsatellite loci polymorphism in ‘somnus’ passion fruit tree (Passiflora setacea DC

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    Douglas de Almeida Pereira

    2015-09-01

    Full Text Available Primer pairs that access microsatellite loci, initially constructed through the genome of Passiflora edulis Sims flavicarpa and P. alata, were tested concerning their ability to access microsatellite loci in ‘somnus’ passion fruit tree (P. setacea individuals. Seven out of the thirty one primer pairs tested were able to access DNA polymorphism in the genome of this wild Passiflora species, by evaluating six natural populations, located in a transition area between the biomes Caatinga and Cerrado, in the state of Bahia, Brazil. The number of alleles/loci was small, oscillating from 1 to 4. The average heterozygosity observed per locus in all populations ranged from 0.13 to 0.40. There was transference of heterologous microsatellite primer pairs from the Passiflora genus to ‘somnus’ passion fruit tree, constituting a new set of primers that access random co-dominant locus in this species, useful for conservationist purposes and pre-improvement of ‘somnus’ passion fruit tree.

  4. Development of nine new microsatellite loci for the American beaver, Castor canadensis (Rodentia: Castoridae), and cross-species amplification in the European beaver, Castor fiber

    Science.gov (United States)

    Pelz-Serrano, K.; Munguia-Vega, A.; Piaggio, A.J.; Neubaum, M.; Munclinger, P.; PArtl, A.; van Riper, Charles; Culver, M.

    2009-01-01

    We developed nine new nuclear dinucleotide microsatellite loci for Castor canadensis. All loci were polymorphic, except for one. The number of alleles ranged from two to four and from five to 12 in populations from Arizona and Wisconsin, respectively. Average heterozygosity ranged from 0.13 to 0.86 per locus. Since cross-species amplification in Castor fiber was successful only in four loci, we tested also nine recently published C. canadensis loci in the Eurasian species. Eight of the published loci amplified; however, three were monomorphic. The number of alleles was lower in C. fiber than in C. canadensis at all loci tested. ?? 2009 Blackwell Publishing Ltd.

  5. Development of ten microsatellite loci in the invasive giant African land snail, Achatina (=Lissachatina) fulica Bowdich, 1822

    Science.gov (United States)

    Morrison, Cheryl L.; Springmann, Marcus J.; Iwanowicz, Deborah D.; Wade, Christopher M.

    2015-01-01

    A suite of tetra-nucleotide microsatellite loci were developed for the invasive giant African land snail, Achatina (=Lissachatina) fulica Bowdich, 1822, from Ion Torrent next-generation sequencing data. Ten of the 96 primer sets tested amplified consistently in 30 snails from Miami, Florida, plus 12 individuals representative of their native East Africa, Indian and Pacific Ocean regions. The loci displayed moderate levels of allelic diversity (average 5.6 alleles/locus) and heterozygosity (average 42 %). Levels of genetic diversity were sufficient to produce unique multi-locus genotypes and detect phylogeographic structuring among regional samples. The invasive A. fulica can cause extensive damage to important food crops and natural resources, including native flora and fauna. The loci characterized here will be useful for determining the origins and tracking the spread of invasions, detecting fine-scale spatial structuring and estimating demographic parameters.

  6. Population study and validation of paternity testing for Thoroughbred horses by 15 microsatellite loci.

    Science.gov (United States)

    Tozaki, T; Kakoi, H; Mashima, S; Hirota, K; Hasegawa, T; Ishida, N; Miura, N; Choi-Miura, N H; Tomita, M

    2001-11-01

    Microsatellite 15 TKY System was characterized for parentage verification of horse registry. The Microsatellite 15 TKY System was constructed by using 15 microsatellites, TKY279, TKY287, TKY294, TKY297, TKY301, TKY312, TKY321, TKY325, TKY333, TKY337, TKY341, TKY343, TKY344, TKY374, and TKY394, to provide stringent PCR-based microsatellite typing specifically optimized for multicolor fluorescence detection. The Microsatellite 15 TKY System showed good resolutions for 250 unrelated Thoroughbred horses, and the probability of exclusion (PE) at each microsatellite ranged from 0.437 to 0.621, resulting in a total PE value of 99.998% for Thoroughbred horses. These results indicated that the Microsatellite 15 TKY System is useful for paternity testing of Thoroughbred horses. A paternity testing case for a Thoroughbred horse family, in which candidate sires had close relations, was analyzed using the Microsatellite 15 TKY System. In this case, the Microsatellite 15 TKY System excluded paternity of a false sire. We concluded that the Microsatellite 15 TKY System can give sufficient and reliable information for paternity testing.

  7. Isolation and characterisation of polymorphic microsatellite loci for Noisy Miners Manorina melanocephala, with successful cross-amplification in Bell Miners M. melanophrys

    NARCIS (Netherlands)

    Kopps, Anna M.; McDonald, Paul; Rollins, Lee Ann

    2013-01-01

    We characterized 15 polymorphic microsatellite loci identified from a Noisy Miner (Manorina melanocephala) blood sample using 454 whole genome shotgun sequencing. Levels of polymorphism were assessed using 15 Noisy Miners. The average number of alleles per locus was 5.1. These loci were then cross-a

  8. Microsatellite Loci in the Gypsophyte Lepidium subulatum (Brassicaceae, and Transferability to Other Lepidieae

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    José Gabriel Segarra-Moragues

    2012-09-01

    Full Text Available Polymorphic microsatellite markers were developed for the Ibero-North African, strict gypsophyte Lepidium subulatum to unravel the effects of habitat fragmentation in levels of genetic diversity, genetic structure and gene flow among its populations. Using 454 pyrosequencing 12 microsatellite loci including di- and tri-nucleotide repeats were characterized in L. subulatum. They amplified a total of 80 alleles (2–12 alleles per locus in a sample of 35 individuals of L. subulatum, showing relatively high levels of genetic diversity, HO = 0.645, HE = 0.627. Cross-species transferability of all 12 loci was successful for the Iberian endemics Lepidium cardamines, Lepidium stylatum, and the widespread, Lepidium graminifolium and one species each of two related genera, Cardaria draba and Coronopus didymus. These microsatellite primers will be useful to investigate genetic diversity, population structure and to address conservation genetics in species of Lepidium.

  9. Phenetic analysis of Trifolium resupinatum L. (Persian clover and Trifolium fragiferum L. (strawberry clover using new microsatellite loci

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    Maryam Haerinasab

    2013-06-01

    Full Text Available Trifolium resupinatum and T. fragiferum are two important crop species among the legumes. T. fragiferum is considered as one of the gene pools of T. resupinatum. In this study, the transferability of SSR markers from T. pratense and T. repens to genotypes of these two species was evaluated and new microsatellite loci for these species were obtained. Their genomic similarity was studied using the SSR markers and phenetic analysis. The results of this study indicated a high level of transferability and polymorphism for microsatellites from T. pratense and T. repens to genotype of T. resupinatum and T. fragiferum. Studies also showed that the genetic diversity was high among the populations and the studied populations were grouped in the low levels of similarity. Also, T. resupinatum and T. fragiferum were grouped in clusters with very low similarity that indicated genomic differences between them in tested SSR loci. This study showed that microsatellites can be useful tools to evaluate genetic variation in these species. The results suggested that as long as specific SSR primers for these two species were not designed, SSR primers of T. pratense and T. repens could be used with high reliability for genomic analysis of these species.

  10. Genetic Characterization of Six Stocks of Litopenaeus vannamei Used in Cuba for Aquaculture by Means of Microsatellite Loci

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    Anna Pérez-Beloborodova

    2012-01-01

    Full Text Available Four microsatellite loci were used to achieve genetic characterization of six stocks from Litopenaeus vannamei used for aquaculture in Cuba: second generation from first introduction (S2-1, first generation from the second one (S1-2, from the third one (S1-3, and the fourth one (S1-4 and the crossings from two parental population: first generation from the first with first generation from the third (S1-1 × S1-3 and first generation from the second with first generation from the third (S1-2 × S1-3. 66% (16/24 of genetic systems in total loci were in genetic disequilibrium. The four microsatellite loci were polymorphic for all six stocks. Major quantities of allelic variants correspond to locus Pvan 1758, which is at the same time that one where there are private alleles from first generation of the third. All Fst comparisons were significant. This indicates big differences between stocks. The highest values are those in which there is presence of the second introduction. This introduction and its descendants are also more consanguineous.

  11. Constraints on Allele size at microsatellite loci : Implications for genetic differentiation

    NARCIS (Netherlands)

    Nauta, M.J.; Weissing, F.J.

    1996-01-01

    Microsatellites are promising genetic markers for studying the demographic structure and phylogenetic history of populations. We present theoretical arguments indicating that the usefulness of microsatellite data for these purposes may be limited to a short time perspective and to relatively small p

  12. Development of Microsatellite Loci in Scrophularia incisa (Scrophulariaceae and Cross-Amplification in Congeneric Species

    Directory of Open Access Journals (Sweden)

    Rui-Hong Wang

    2014-02-01

    Full Text Available Premise of the study: To elucidate the population genetics and phylogeography of Scrophularia incisa, microsatellite primers were developed. We also applied these microsatellite markers to its closely related species S. dentata and S. kiriloviana. Methods and Results: Using the compound microsatellite marker technique, 12 microsatellite primers were identified in S. incisa. The number of alleles ranged from 14 to 26 when assessed in 78 individuals from four populations. With high cross-species transferability, these primers also amplified in S. dentata and S. kiriloviana. Conclusions: These results indicate that these microsatellite markers are adequate for detecting and characterizing population genetic structure in the Chinese species of sect. Tomiophyllum at fine and range-wide geographical scales.

  13. Genetic Characterization of Six Stocks of Litopenaeus vannamei Used in Cuba for Aquaculture by Means of Microsatellite Loci

    OpenAIRE

    Anna Pérez-Beloborodova; Adriana Artiles-Valor; Lourdes Pérez-Jar; Damir Hernández-Martínez; Missael Guerra-Aznay; Georgina Espinosa-López

    2012-01-01

    Four microsatellite loci were used to achieve genetic characterization of six stocks from Litopenaeus vannamei used for aquaculture in Cuba: second generation from first introduction (S2-1), first generation from the second one (S1-2), from the third one (S1-3), and the fourth one (S1-4) and the crossings from two parental population: first generation from the first with first generation from the third (S1-1 × S1-3) and first generation from the second with first generation from the third (S1...

  14. Isolation and characterization of microsatellite loci for the herbaceous tuber crop, Amorphophallus konjac (Araceae).

    Science.gov (United States)

    Pan, C; You, Y N; Diao, Y; Hu, Z L; Chen, J M

    2012-12-19

    Amorphophallus konjac is an herbaceous tuber crop with tremendous potential for commercial development. We report the development of microsatellite primers for this important crop species. Thirteen polymorphic microsatellite markers were developed and tested in two populations of A. konjac from the Wuling Mountain Region (WL population) and the Yunnan Province (YN population) in China. The number of alleles per locus ranged from 1 to 7; the observed and expected heterozygosities ranged from 0 to 1 and from 0 to 0.844, respectively, in the two populations. These microsatellite markers will facilitate further studies in population genetics and utilization of A. konjac.

  15. Isolation and characterization of microsatellite DNA loci in the threatened flat-spired three-toothed land snail Triodopsis platysayoides

    Science.gov (United States)

    King, Timothy L.; Eackles, Michael S.; Garner, B. A.; van Tuinen, M.; Arbogast, B. S.

    2015-01-01

    The hermaphroditic flat-spired three-tooth land snail (Triodopsis platysayoides) is endemic to a 21-km stretch of the Cheat River Gorge of northeastern West Virginia, USA. We document isolation and characterization of ten microsatellite DNA markers in this at-risk species. The markers displayed a moderate level of allelic diversity (averaging 7.1 alleles/locus) and heterozygosity (averaging 58.6 %). Allelic diversity at seven loci was sufficient to produce unique multilocus genotypes; no indication of selfing was detected in this cosexual species. Minimal deviations from Hardy–Weinberg equilibrium and no linkage disequilibrium were observed within subpopulations. All loci deviated from Hardy–Weinberg expectations when individuals from subpopulations were pooled. Microsatellite markers developed for T. platysayoides yielded sufficient genetic diversity to (1) distinguish all individuals sampled and the level of selfing; (2) be appropriate for addressing fine-scale population structuring; (3) provide novel demographic insights for the species; and (4) cross-amplify and detect allelic diversity in the congeneric T. juxtidens.

  16. Selecting representative microsatellite loci for genetic monitoring and analyzing genetic structure of an outbred population of orange tabby cats in China.

    Science.gov (United States)

    Du, X Y; Yi, S; Huo, X Y; Wang, C; Liu, D F; Ren, W Z; Chen, Z W

    2015-03-13

    We optimized a panel of microsatellite markers from cat and tiger genetic data for efficient genetic monitoring and used it to analyze the genetic structure of an outbred cat stock in China. We selected a set of rich polymorphic microsatellite loci from 131 cat microsatellite loci and 3 Sumatran tiger microsatellite loci using agarose gel electrophoresis. Next, the set of optimized genetic markers was used to analyze the genetic variation in an outbred population of orange tabby cats in China by simple-tandem repeat scanning. Thirty-one loci rich in polymorphisms were selected and the highest allele number in a single locus was 8. Analysis of the orange tabby cat population illustrated that the average observed number of alleles, mean effective allele number, mean Shannon's information index, mean expected heterozygosity, and observed heterozygosity were 3.8387, 2.4027, 0.9787, 0.5565, and 0.5528, respectively. The 31 microsatellite markers used were polymorphic and suitable for analyzing the genetic structure of cats. The population of orange tabby cats was confirmed to be a well-outbred stock.

  17. Characterization of microsatellite loci in the lichen-forming fungus Cetraria aculeata (Parmeliaceae, Ascomycota).

    Science.gov (United States)

    Lutsak, Tetiana; Fernández-Mendoza, Fernando; Greshake, Bastian; Dal Grande, Francesco; Ebersberger, Ingo; Ott, Sieglinde; Printzen, Christian

    2016-09-01

    Polymorphic microsatellite markers were developed for the lichen species Cetraria aculeata (Parmeliaceae) to study fine-scale population diversity and phylogeographic structure. Using Illumina HiSeq and MiSeq, 15 fungus-specific microsatellite markers were developed and tested on 81 specimens from four populations from Spain. The number of alleles ranged from four to 13 alleles per locus with a mean of 7.9, and average gene diversities varied from 0.40 to 0.73 over four populations. The amplification rates of 10 markers (CA01-CA10) in populations of C. aculeata exceeded 85%. The markers also amplified across a range of closely related species, except for locus CA05, which did not amplify in C. australiensis and C. "panamericana," and locus CA10 which did not amplify in C. australiensis. The identified microsatellite markers will be used to study the genetic diversity and phylogeographic structure in populations of C. aculeata in western Eurasia.

  18. Identification and validation of polymorphic microsatellite loci for the analysis of Phytophthora nicotianae populations

    Science.gov (United States)

    A large number of SSR loci were screened in the genomic assemblies of 14 different isolates of Phytophthora nicotianae and primers were developed for amplification of 17 markers distributed among different contigs. These loci were highly polymorphic and amplified from genetically distant isolates of...

  19. Chromosomal locations of four minor rDNA loci and a marker microsatellite sequence in barley

    DEFF Research Database (Denmark)

    Pedersen, C.; Linde-Laursen, I.

    1994-01-01

    is located about 54% out on the short arm of chromosome 4 and it has not previously been reported in barley. We have designated the new locus Nor-I6. rDNA loci on homoeologous group 4 chromosomes have not yet been reported in other Triticeae species. The origin of these 4 minor rDNA loci is discussed...

  20. Development and characterization of 17 polymorphic microsatellite loci in the faucet snail, Bithynia tentaculata (Gastroposa: Caenogastropoda; Bithyniidae)

    Science.gov (United States)

    Henningsen, Justin P.; Lance, Stacey L.; Jones, Kenneth L.; Hagen, Chris; Laurila, Joshua; Cole, Rebecca A.; Perez, Kathryn E.

    2010-01-01

    Bithynia tentaculata (Linnaeus, 1758), a snail native to Europe, was introduced into the US Great Lakes in the 1870's and has spread to rivers throughout the Northeastern US and Upper Mississippi River (UMR). Trematode parasites, for which B. tentaculata is a host, have also been introduced and are causing widespread waterfowl mortality in the UMR. Waterfowl mortality is caused by ingestion of trematode-infected B. tentaculata or insects infected with parasites released from the snails. We isolated and characterized 17 microsatellite loci from the invasive faucet snail, B. tentaculata (Gastropoda: Caenogastropoda: Bithyniidae). Loci were screened in 24 individuals of B. tentaculata. The number of alleles per locus ranged from 2 to 6, observed heterozygosity ranged from 0.050 to 0.783, and the probability of identity values ranged from 0.10 to 0.91. These new loci provide tools for examining the origin and spread of invasive populations in the US and management activities to prevent waterfowl mortality.

  1. Characterization of thirteen microsatellite loci from the Ghanian antimalarial plant Cryptolepis sanguinolenta

    Science.gov (United States)

    Cryptolepis sanguinolenta (Lindl.) Schlechter (Periplocaceae) is an herbaceous plant used in traditional medicine to treat malaria and populations of the species are diminishing due to overharvesting and lack of conservation. Co-dominant microsatellite markers that can be used to characterize geneti...

  2. Isolation of polymorphic microsatellite loci from the flea beetle Phyllotreta nemorum L. (Coleoptera: Chrysomelidae)

    NARCIS (Netherlands)

    Verbaarschot, P.G.H.; Calvo, D.; Esselink, G.D.; Molina, J.M.; Vrieling, K.; Jong, de P.W.

    2007-01-01

    Ten microsatellite markers for the flea beetle Phyllotreta nemorum were developed using di- and trinucleotide repeat-enriched libraries. Each of these primer pairs were characterized on 96 individuals. Expected heterozygosities ranged between 0.11 and 0.84 and the number of alleles ranged between tw

  3. Isolation and characterization of microsatellite loci in tropical forage Stylosanthes capitata Vogel.

    Science.gov (United States)

    Santos, M O; Sassaki, R P; Chiari, L; Resende, R M S; DE Souza, A P

    2009-01-01

    Stylosanthes capitata is an important tropical pasture legume. Knowledge of genetic diversity and structure of S. capitata populations is of great importance for the conservation and germplasm management of this species. Thus, eight microsatellite markers were developed from an S. capitata-enriched library. They were characterized in 20 accessions from the germplasm collection of the Empresa Brasileira de Pesquisa Agropecuária (Embrapa). The observed and expected heterozygosities ranged from 0.16 to 0.85 and from 0.40 to 0.85, respectively. These microsatellites are the first set of molecular markers from this species and will contribute towards studies of genetic diversity, conservation and breeding of S. capitata.

  4. Isolation and Characterization of Microsatellite Loci in the Invasive Herb Solidago altissima (Asteraceae

    Directory of Open Access Journals (Sweden)

    Yuzu Sakata

    2013-04-01

    Full Text Available Premise of the study: Microsatellite markers were developed in the perennial herb Solidago altissima from populations within its introduced range in Japan to assess its population structure and to facilitate tracking of invasion expansion. Methods and Results: Using 454 pyrosequencing, 16 microsatellite primer sets were developed for S. altissima. The primer sets were tested on 70 individuals sampled from three populations in Japan. The primers amplified di- and trinucleotide repeats with five to 25 alleles per locus, and the expected heterozygosity ranged from 0.46 to 0.92. Conclusions: These results indicate the utility of primers in S. altissima for future research on a wide range of applications, including tracking of invasion dynamics and investigating population genetics of the species.

  5. Isolation and characterization of microsatellite loci in the invasive herb Solidago altissima (Asteraceae)1

    Science.gov (United States)

    Sakata, Yuzu; Kaneko, Shingo; Hayano, Azusa; Inoue-Murayama, Miho; Ohgushi, Takayuki; Isagi, Yuji

    2013-01-01

    • Premise of the study: Microsatellite markers were developed in the perennial herb Solidago altissima from populations within its introduced range in Japan to assess its population structure and to facilitate tracking of invasion expansion. • Methods and Results: Using 454 pyrosequencing, 16 microsatellite primer sets were developed for S. altissima. The primer sets were tested on 70 individuals sampled from three populations in Japan. The primers amplified di- and trinucleotide repeats with five to 25 alleles per locus, and the expected heterozygosity ranged from 0.46 to 0.92. • Conclusions: These results indicate the utility of primers in S. altissima for future research on a wide range of applications, including tracking of invasion dynamics and investigating population genetics of the species. PMID:25202531

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Kristjan Jarni

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

  8. Microsatellite loci isolation from river buffalo using enriched partial genomic libraries

    Directory of Open Access Journals (Sweden)

    A.L. Silva

    2010-02-01

    Full Text Available The extensive use of buffalo in agriculture, especially in developing countries, begs for genetic resources to evaluate and improve traits important to local and regional economies. Brazil presents the largest water buffalo populations in the New World, with 1.1 million heads including swamp and river types. To design rational breeding strategies for optimum utilization and conservation of available genetic variability in the Brazilian buffalo’s population, it is essential to understand their genetic architecture and relationship among various breeds. This depends, in part, on the knowledge of their genetic structure based on molecular markers like microsatellites. In the present study, we developed six enriched partial genomic libraries for river buffalo using selective hybridization methods. Genomic DNA was hybridized with six different arrays of repeat motif, 5’ biotinylated - (CA15, (CT15, (AGG8, (GAAA8, (GATA8, (AAAAC8 – and bound to streptavidin coated beads. The cloning process generated a total of 1920 recombinant clones. Up to date, 487 were directly sequenced for the presence of repeats, from which 13 have been positive for presence of repeats as follows: 9 for di-nucleotide repeats, 3 for tri-nucleotide repeats and 1 for tetra-nucleotide repeat. PCR primer pairs for the isolated microsatellites are under construction to determine optimum annealing temperature. These microsatellites will be useful for studies involving phylogenetic relationships, genome mapping and genetic diversity analysis within buffalo populations worldwide.

  9. Characterization of microsatellite loci in the lichen-forming fungus Cetraria aculeata (Parmeliaceae, Ascomycota)1

    Science.gov (United States)

    Lutsak, Tetiana; Fernández-Mendoza, Fernando; Greshake, Bastian; Dal Grande, Francesco; Ebersberger, Ingo; Ott, Sieglinde; Printzen, Christian

    2016-01-01

    Premise of the study: Polymorphic microsatellite markers were developed for the lichen species Cetraria aculeata (Parmeliaceae) to study fine-scale population diversity and phylogeographic structure. Methods and Results: Using Illumina HiSeq and MiSeq, 15 fungus-specific microsatellite markers were developed and tested on 81 specimens from four populations from Spain. The number of alleles ranged from four to 13 alleles per locus with a mean of 7.9, and average gene diversities varied from 0.40 to 0.73 over four populations. The amplification rates of 10 markers (CA01–CA10) in populations of C. aculeata exceeded 85%. The markers also amplified across a range of closely related species, except for locus CA05, which did not amplify in C. australiensis and C. “panamericana,” and locus CA10 which did not amplify in C. australiensis. Conclusions: The identified microsatellite markers will be used to study the genetic diversity and phylogeographic structure in populations of C. aculeata in western Eurasia. PMID:27672520

  10. Microsatellites from the charcoal rot fungus (Macrophomina phaseolina).

    Science.gov (United States)

    Baird, Richard E; Wadl, Phillip A; Wang, Xinwang; Johnson, Denita H; Rinehart, Timothy A; Abbas, Hamed K; Shier, Thomas; Trigiano, Robert N

    2009-05-01

    Microsatellite loci were identified from the charcoal rot fungus (Macrophomina phaseolina). Primer pairs for 46 loci were developed, and of these, 13 were optimized and screened using genomic DNA from 55 fungal isolates collected predominantly from two soybean fields in Mississippi. Twelve of the optimized loci were polymorphic and the number of alleles per locus ranged from 6 to 22. These microsatellites will be useful in population and pathogenicity studies to correspond with development of potential disease-resistant soybean and other susceptible crops. © 2009 Blackwell Publishing Ltd. No claim to original US government works.

  11. Characterisation of a novel panel of polymorphic microsatellite loci for the liver fluke, Fasciola hepatica, using a next generation sequencing approach.

    Science.gov (United States)

    Cwiklinski, Krystyna; Allen, Katherine; LaCourse, James; Williams, Diana J; Paterson, Steve; Hodgkinson, Jane E

    2015-06-01

    The liver fluke, Fasciola hepatica is an economically important pathogen of sheep and cattle and has been described by the WHO as a re-emerging zoonosis. Control is heavily reliant on the use of drugs, particularly triclabendazole and as a result resistance has now emerged. The population structure of F. hepatica is not well known, yet it can impact on host-parasite interactions and parasite control with drugs, particularly regarding the spread of triclabendazole resistance. We have identified 2448 potential microsatellites from 83 Mb of F. hepatica genome sequence using msatfinder. Thirty-five loci were developed and optimised for microsatellite PCR, resulting in a panel of 15 polymorphic loci, with a range of three to 15 alleles. This panel was validated on genomic DNA from 46 adult F. hepatica; 38 liver flukes sourced from a Northwest abattoir, UK and 8 liver flukes from an established isolate (Shrewsbury; Ridgeway Research). Evidence for null alleles was found at four loci (Fh_1, Fh_8, Fh_13 and Fh_14), which showed markedly higher levels of homozygosity than the remaining 11 loci. Of the 38 liver flukes isolated from cattle livers (n=10) at the abattoir, 37 genotypes were identified. Using a multiplex approach all 15 loci could be amplified from several life cycle stages that typically yield low amounts of DNA, including metacercariae, the infective life cycle stage present on pasture, highlighting the utility of this multiplex microsatellite panel. This study reports the largest panel of microsatellite markers available to date for population studies of F. hepatica and the first multiplex panel of microsatellite markers that can be used for several life cycle stages.

  12. Characterisation of a novel panel of polymorphic microsatellite loci for the liver fluke, Fasciola hepatica, using a next generation sequencing approach☆

    Science.gov (United States)

    Cwiklinski, Krystyna; Allen, Katherine; LaCourse, James; Williams, Diana J.; Paterson, Steve; Hodgkinson, Jane E.

    2015-01-01

    The liver fluke, Fasciola hepatica is an economically important pathogen of sheep and cattle and has been described by the WHO as a re-emerging zoonosis. Control is heavily reliant on the use of drugs, particularly triclabendazole and as a result resistance has now emerged. The population structure of F. hepatica is not well known, yet it can impact on host–parasite interactions and parasite control with drugs, particularly regarding the spread of triclabendazole resistance. We have identified 2448 potential microsatellites from 83 Mb of F. hepatica genome sequence using msatfinder. Thirty-five loci were developed and optimised for microsatellite PCR, resulting in a panel of 15 polymorphic loci, with a range of three to 15 alleles. This panel was validated on genomic DNA from 46 adult F. hepatica; 38 liver flukes sourced from a Northwest abattoir, UK and 8 liver flukes from an established isolate (Shrewsbury; Ridgeway Research). Evidence for null alleles was found at four loci (Fh_1, Fh_8, Fh_13 and Fh_14), which showed markedly higher levels of homozygosity than the remaining 11 loci. Of the 38 liver flukes isolated from cattle livers (n = 10) at the abattoir, 37 genotypes were identified. Using a multiplex approach all 15 loci could be amplified from several life cycle stages that typically yield low amounts of DNA, including metacercariae, the infective life cycle stage present on pasture, highlighting the utility of this multiplex microsatellite panel. This study reports the largest panel of microsatellite markers available to date for population studies of F. hepatica and the first multiplex panel of microsatellite markers that can be used for several life cycle stages. PMID:25796359

  13. Isolation of polymorphic microsatellite loci for the marine invader Microcosmus squamiger (Ascidiacea).

    Science.gov (United States)

    Rius, Marc; Turon, Xavier; Pascual, Marta

    2008-11-01

    The ascidian Microcosmus squamiger is native to Australia and has recently spread worldwide. It has become a pest in some littoral communities within its introduced range. An enriched genomic library of M. squamiger resulted in a total of eight polymorphic loci that were genotyped in 20 individuals from a population within its introduced range, and 20 individuals more from a native population. The mean number of alleles per locus was 5.33 and mean observed heterozygosity was 0.432. No significant linkage disequilibrium was found among loci pairs. Significant genetic differentiation was observed between populations.

  14. Development of 11 microsatellite loci for an endangered herb, Paraisometrum mileense (Gesneriaceae), in southwest China.

    Science.gov (United States)

    Tang, An-Jun; Zhou, Ren-Chao; Ge, Xue-Jun; Wu, Wei

    2013-01-01

    Microsatellite markers were developed to investigate the genetic diversity and population structure of the endangered species Paraisometrum mileense, as well as its evolutionary history. • Using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol, 11 polymorphic primer sets were obtained in P. mileense. The number of alleles per locus ranged from one to nine with an average 3.8, and the observed and expected heterozygosities ranged from 0 to 1 and 0 to 0.89, respectively, for the available three populations. • These markers may be useful for further investigation of the conservation genetics of P. mileense.

  15. Development of 11 Microsatellite Loci for an Endangered Herb, Paraisometrum mileense (Gesneriaceae, in Southwest China

    Directory of Open Access Journals (Sweden)

    An-Jun Tang

    2013-01-01

    Full Text Available Premise of the study: Microsatellite markers were developed to investigate the genetic diversity and population structure of the endangered species Paraisometrum mileense, as well as its evolutionary history. Methods and Results: Using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO protocol, 11 polymorphic primer sets were obtained in P. mileense. The number of alleles per locus ranged from one to nine with an average 3.8, and the observed and expected heterozygosities ranged from 0 to 1 and 0 to 0.89, respectively, for the available three populations. Conclusions: These markers may be useful for further investigation of the conservation genetics of P. mileense.

  16. Development of 11 microsatellite loci for an endangered herb, Paraisometrum mileense (Gesneriaceae), in southwest China1

    Science.gov (United States)

    Tang, An-Jun; Zhou, Ren-Chao; Ge, Xue-Jun; Wu, Wei

    2013-01-01

    • Premise of the study: Microsatellite markers were developed to investigate the genetic diversity and population structure of the endangered species Paraisometrum mileense, as well as its evolutionary history. • Methods and Results: Using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol, 11 polymorphic primer sets were obtained in P. mileense. The number of alleles per locus ranged from one to nine with an average 3.8, and the observed and expected heterozygosities ranged from 0 to 1 and 0 to 0.89, respectively, for the available three populations. • Conclusions: These markers may be useful for further investigation of the conservation genetics of P. mileense. PMID:25202475

  17. Genetic structure of Indian populations based on fifteen autosomal microsatellite loci

    Directory of Open Access Journals (Sweden)

    Bindu G Hima

    2006-05-01

    Full Text Available Abstract Background Indian populations endowed with unparalleled genetic complexity have received a great deal of attention from scientists world over. However, the fundamental question over their ancestry, whether they are all genetically similar or do exhibit differences attributable to ethnicity, language, geography or socio-cultural affiliation is still unresolved. In order to decipher their underlying genetic structure, we undertook a study on 3522 individuals belonging to 54 endogamous Indian populations representing all major ethnic, linguistic and geographic groups and assessed the genetic variation using autosomal microsatellite markers. Results The distribution of the most frequent allele was uniform across populations, revealing an underlying genetic similarity. Patterns of allele distribution suggestive of ethnic or geographic propinquity were discernible only in a few of the populations and was not applicable to the entire dataset while a number of the populations exhibited distinct identities evident from the occurrence of unique alleles in them. Genetic substructuring was detected among populations originating from northeastern and southern India reflective of their migrational histories and genetic isolation respectively. Conclusion Our analyses based on autosomal microsatellite markers detected no evidence of general clustering of population groups based on ethnic, linguistic, geographic or socio-cultural affiliations. The existence of substructuring in populations from northeastern and southern India has notable implications for population genetic studies and forensic databases where broad grouping of populations based on such affiliations are frequently employed.

  18. Genetic diversity in a Brazilian bovine herd based on four microsatellite loci

    Directory of Open Access Journals (Sweden)

    Almeida Sabrina E. Matos

    2000-01-01

    Full Text Available Microsatellites or short tandem repeats (STRs, DNA markers relatively abundant in the genome, have a high degree of polymorphism and therefore great potential for characterizing populations. The present study estimates genetic variability in a set of four microsatellites (BMS3013, BMS3004, HEL10 and TGLA122 in a Brazilian hybrid bovine breed (5/8 Aberdeen Angus x 3/8 Nelore. The objectives were to determine the effect of crossbreeding and selection in these animals' genetic diversity as well as to discover the herd's genetic relationship with that of other breeds. Low diversity was verified in BMS3013 and high diversity was detected in BMS3004, HEL10 and TGLA122. Two alleles in TGLA122 are described here for the first time (TGLA122*155 and TGLA122*163. These genes are possibly characteristics of Zebu animals since they have not been found in other taurine samples so far investigated. Low interpopulational diversity was observed among taurine cattle populations, and clusters obtained on TGLA122 phylogenetic trees agreed with the bovine herd's geographic origin. Therefore, despite TGLA122's high polymorphism and high levels of intrapopulational diversity, the system engenders consistent bovine phylogenies. We detected an intriguingly high similarity between Brangus Ibagé and Red Angus since the former is a hybrid having 3/8 of Nelore genes. Either these animals' environment or genetic selective practices applied to the breed probably favor the Angus genotype.

  19. Microplate array diagonal gel electrophoresis for cohort studies of microsatellite loci.

    Science.gov (United States)

    Chen, Xiao-he; O'Dell, Sandra D; Day, Ian N M

    2002-05-01

    After PCR amplification, we have achieved precise sizing of trinucleotide and tetranucleotide microsatellite alleles on 96-well open-faced polyacrylamide microplate array diagonal gel electrophoresis (MADGE) gels: two tetranucleotide repeats, HUMTHOI (five alleles 248-263 bp) and DYS390 (eight alleles 200-228 bp), and DYS392, a trinucleotide repeat (eight alleles 210-231 bp). A gel matrix of Duracryl, a high mechanical strength polyacrylamide derivative, and appropriate ionic conditions provide the 1.3%-1.5% band resolution required. No end-labeling of primers is needed, as the sensitive Vistra Green intercalating dye is used for the visualization of bands. Co-run markers bracketing the PCR fragments ensure accurate sizing without inter-lane variability. Electrophoresis of multiple gels in a thermostatically controlled tank allows up to 1000 samples to be run in 90 min. Gel images were analyzed using a Fluorlmager 595 fluorescent scanning system, and alleles were identified using Phoretix software for band migration measurement and Microsoft Excel to compute fragment sizes. Estimated sizes were interpolated precisely to achieve accurate binning. Microsatellite-MADGE represents a utilitarian methodfor high-throughput genotyping in cohort studies, using standard laboratory equipment.

  20. GENETIC STRUCTURE AND ALLEL DIVERSITY OF THREE BALINESE GENERATIONS BASED ON FIVE AUTOSOMAL MICROSATELLITE DNA LOCI

    Directory of Open Access Journals (Sweden)

    Ayu Saka Laksmita

    2015-09-01

    Full Text Available This research was aimed to find out the genetic structures of three generations of Balinese population, in order to determine the best loci used for paternity testing among this population, and observed the mutation rate of these loci. The DNA samples were taken from the epithelium cell of 25 families which were collected from the children, father, mother, grandfather and grandmother of the children, from both mother and father sides (family with three generations. The DNA was extracted in Phenol-Chloroform method with modifications. DNA amplification was conducted in PCR method using pairs of primer 5, namely: FGA, D18S51, D2S1338, TPOX, and D16S539, and its products were electrophoresed and visualized in 10% of PAGE, stained in silver nitrate. The genetic structures of the three family generations showed 30 variants with different frequencies in each locus. The highest heterozygosity value was detected in FGA (8 alleles, then followed by D18S51 (7 alleles, TPOX (6 alleles, D16S539 (5 alleles, and the lowest was in D2S1338 (4 alleles. The highest value of heterozigosity and Power of Discrimination were found in FGA, followed by TPOX, D18S51, D2S1338, and the lowest was in D16S539. Therefore, it can be concluded that out of five loci tested, 4 of them can be recommended to be used for paternity testing of Balinese population, except D16S539

  1. Isolation and characterization of polymorphic microsatellite loci for Siphamia tubifer Weber (Perciformes: Apogonidae)

    KAUST Repository

    Alpermann, Tilman J.

    2014-07-14

    The cardinalfish Siphamia tubifer has been selected as a model for the study of genetic connectivity in reef-associated fishes among marine-protected-areas in Socotra Island in the northwestern Indian Ocean (part of the Socotra Archipelago, a UNESCO World Heritage Site since 2008). Twenty-six novel microsatellite markers are described for S. tubifer and are now available for studies on its genetic population structure. In a population sample from Socotra Island, the newly developed markers possessed between three and 20 alleles. Expected and observed heterozygosity ranged from 0.56–0.96 to 0.55–0.95, respectively. The markers did not show deviations from Hardy–Weinberg equilibrium and were not in linkage disequilibrium.

  2. SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera).

    Science.gov (United States)

    Muñoz, Irene; Henriques, Dora; Jara, Laura; Johnston, J Spencer; Chávez-Galarza, Julio; De La Rúa, Pilar; Pinto, M Alice

    2016-11-14

    The honeybee (Apis mellifera) has been threatened by multiple factors including pests and pathogens, pesticides and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A. m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify pure-bred A. m. mellifera colonies. Microsatellites have been preferred for identification of A. m. mellifera stocks across conservation centres. However, owing to high throughput, easy transferability between laboratories and low genotyping error, SNPs promise to become popular. Here, we compared the resolving power of a widely utilized microsatellite set to detect structure and introgression with that of different sets that combine a variable number of SNPs selected for their information content and genomic proximity to the microsatellite loci. Contrary to every SNP data set, microsatellites did not discriminate between the two lineages in the PCA space. Mean introgression proportions were identical across the two marker types, although at the individual level, microsatellites' performance was relatively poor at the upper range of Q-values, a result reflected by their lower precision. Our results suggest that SNPs are more accurate and powerful than microsatellites for identification of A. m. mellifera colonies, especially when they are selected by information content.

  3. Characterization of six microsatellite loci in Myrica faya (Myricaceae and cross amplification in the endangered endemic M. rivas-martinezii in Canary Islands, Spain

    Directory of Open Access Journals (Sweden)

    Miguel A. González-Pérez

    2009-01-01

    Full Text Available Six novel polymorphic microsatellite markers were isolated from enriched libraries in Myrica faya Ait., recently renamed Morella faya , (fayatree, firetree, or firebush in order to examine the genetic diversity in natural populations. Also, test cross-specific amplification and genetic diversity in Myrica rivas-martinezii, which is endemic on the Canary islands. Microsatellite loci were screened in 225 individuals of both species from different islands of the Canarian archipelago. All markers were successfully amplified from both Myrica species, with an average number of 6.5 and 9.3 alleles per locus in M. rivas-martinezii and M. faya , respectively. There was no evidence for linkage disequilibrium between loci, and the probability of null alleles ranged from 0.01 to 0.17.

  4. Novel Microsatellite Markers for Brazilian Mangrove Oysters ( Crassostrea gasar ) and their Cross-Amplification in Crassostrea rhizophorae

    OpenAIRE

    Baldez,Renata do Socorro Corrêa; Melo,Mauro André Damasceno; Sampaio, Iracilda; TAGLIARO, Claudia Helena

    2016-01-01

    ABSTRACT A microsatellite CT/GT enriched genomic library was developed for Crassostrea gasar and twelve new polymorphic loci were isolated and characterized. The markers were successfully amplified from 25 individuals of Crassostrea gasar and 11 cross-amplified individuals of Crassostrea rhizophorae. There was no evidence of linkage between loci in either species.

  5. 'True' null allele detection in microsatellite loci: a comparison of methods, assessment of difficulties and survey of possible improvements.

    Science.gov (United States)

    Dąbrowski, M J; Bornelöv, S; Kruczyk, M; Baltzer, N; Komorowski, J

    2015-05-01

    Null alleles are alleles that for various reasons fail to amplify in a PCR assay. The presence of null alleles in microsatellite data is known to bias the genetic parameter estimates. Thus, efficient detection of null alleles is crucial, but the methods available for indirect null allele detection return inconsistent results. Here, our aim was to compare different methods for null allele detection, to explain their respective performance and to provide improvements. We applied several approaches to identify the 'true' null alleles based on the predictions made by five different methods, used either individually or in combination. First, we introduced simulated 'true' null alleles into 240 population data sets and applied the methods to measure their success in detecting the simulated null alleles. The single best-performing method was ML-NullFreq_frequency. Furthermore, we applied different noise reduction approaches to improve the results. For instance, by combining the results of several methods, we obtained more reliable results than using a single one. Rule-based classification was applied to identify population properties linked to the false discovery rate. Rules obtained from the classifier described which population genetic estimates and loci characteristics were linked to the success of each method. We have shown that by simulating 'true' null alleles into a population data set, we may define a null allele frequency threshold, related to a desired true or false discovery rate. Moreover, using such simulated data sets, the expected null allele homozygote frequency may be estimated independently of the equilibrium state of the population.

  6. Multiplexed microsatellite loci in American crow (Corvus brachyrhynchos): a severely affected natural host of West Nile virus.

    Science.gov (United States)

    Verdugo, Claudio; Clark, Ann Marie; Prakoso, Dhani; Kramer, Laura D; Long, Maureen T

    2012-12-01

    Recent advances in high throughput molecular techniques have allowed the development of cost- and time-effective libraries of molecular markers, such as microsatellites, for population genetic studies in non-model species. The American crow, Corvus brachyrhynchos, is recognized to be one of the species that has been most negatively affected by the emergence of West Nile virus (WNV) in North America in 1999. Genetic monitoring of the process of a declining population after the introduction of an infectious disease can provide insights into the demographic and evolutionary impact of a pathogen in a natural host population over time. In this study, shotgun pyrosequencing and validation of previously published cross-species markers were the approaches used to identify and develop a set of 32 polymorphic loci for the C. brachyrhynchos. Since the American crow is morphologically similar to the sympatric species Fish crow (Corvus ossifragus), we also designed a real-time PCR protocol to rapidly differentiate these two species using a set of primers and probes that can discriminate a section of the COI gene at the mitochondrial DNA. These new markers together with a faster method for species verification will allow further detailed studies to characterize and compare genetic diversity of historic and contemporary C. brachyrhynchos populations. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Location of Vibrio anguillarum resistance-associated trait loci in half-smooth tongue sole Cynoglossus semilaevis at its microsatellite linkage map

    Science.gov (United States)

    Tang, Zhihong; Guo, Li; Liu, Yang; Shao, Changwei; Chen, Songlin; Yang, Guanpin

    2016-11-01

    A cultured female half-smooth tongue sole ( Cynoglossus semilaevis) was crossed with a wild male, yielding the first filial generation of pseudo-testcrossing from which 200 fish were randomly selected to locate the Vibrio anguillarum resistance trait in half-smooth tongue sole at its microsatellite linkage map. In total, 129 microsatellites were arrayed into 18 linkage groups, ≥4 each. The map reconstructed was 852.85 cM in length with an average spacing of 7.68 cM, covering 72.07% of that expected (1 183.35 cM). The V. anguillarum resistance trait was a composite rather than a unit trait, which was tentatively partitioned into Survival time in Hours After V. anguillarum Infection (SHAVI) and Immunity of V. Anguillarum Infection (IVAI). Above a logarithm of the odds (LOD) threshold of 2.5, 18 loci relative to SHAVI and 3 relative to IVAI were identified. The 3 loci relative to IVAI explained 18.78%, 5.87% and 6.50% of the total phenotypic variation in immunity. The microsatellites bounding the 3 quantitative trait loci (QTLs) of IVAI may in future aid to the selection of V. anguillarum-immune half-smooth tongue sole varieties, and facilitate cloning the gene(s) controlling such immunity.

  8. Genetic structuring in a relictual population of screaming hairy armadillo (Chaetophractus vellerosus) in Argentina revealed by a set of novel microsatellite loci.

    Science.gov (United States)

    Nardelli, Maximiliano; Ibáñez, Ezequiel Alejandro; Dobler, Dara; Justy, Fabienne; Delsuc, Frédéric; Abba, Agustín Manuel; Cassini, Marcelo Hernán; Túnez, Juan Ignacio

    2016-08-01

    The screaming hairy armadillo (Chaetophractus vellerosus) is a mammal species containing disjunct and isolated populations. In order to assess the effect of habitat fragmentation and geographic isolation, we developed seven new microsatellite loci isolated from low-coverage genome shotgun sequencing data for this species. Among these loci, six microsatellites were found to be polymorphic with 8-26 alleles per locus detected across 69 samples analyzed from a relictual population of the species located in the northeast of the Buenos Aires Province (Argentina). Mean allelic richness and polymorphic information content were 15 and 0.75, with observed and expected heterozygosities ranging from 0.40 to 0.67 and 0.58 to 0.90, respectively. All loci showed departures from Hardy-Weinberg equilibrium. The analysis of population structure in this relictual population revealed three groups of individuals that are genetically differentiated. These newly developed microsatellites will constitute a very useful tool for the estimation of genetic diversity and structure, population dynamics, social structure, parentage and mating system in this little-studied armadillo species. Such genetic data will be particularly helpful for the development of conservation strategies for this isolated population and also for the endangered Bolivian populations previously recognized as a distinct species (Chaetophractus nationi).

  9. Genetic variability and heterogeneity of Venezuelan equine encephalitis virus vector Ochlerotatus taeniorhynchus (Diptera: Culicidae) populations of the Colombian Atlantic coast, based on microsatellite loci.

    Science.gov (United States)

    Bello, F; Becerra, V

    2009-09-29

    In Colombia, the mosquito Ochlerotatus taeniorhynchus has been identified as an efficient vector of the epidemic-epizootic Venezuelan equine encephalitis virus. We evaluated the genetic variability and heterogeneity of this mosquito in Colombian populations using eight microsatellite DNA loci. Two hundred and ten mosquito specimens collected from seven populations of the Colombian Atlantic coast (San Bernardo del Viento, Coveñas, Cartagena, Barranquilla, Ciénaga, Dibulla, and Riohacha) were analyzed. We found five polymorphic microsatellite loci, with 19 alleles giving 62.5% polymorphism; the mean number of alleles per locus was 3.8. The mean expected heterogeneity ranged from 0.568 to 0.660. Most of the polymorphic microsatellite loci were in Hardy-Weinberg disequilibrium, due to both deficit and excess of heterozygotes. The Fst statistic gave a total value of 0.0369, reflecting low genetic differentiation among the populations and, as a consequence, a low degree of structuring among them, while gene flow was high (Nm = 6.52); these findings point to genetic homogeneity among these populations. There was no significant linkage disequilibrium between genotype pairs of the various populations. We concluded that this mosquito is distributed in local populations along the Colombian Atlantic coast; these findings will be useful for developing strategies for controlling this vector.

  10. Segregation of microsatellite alleles and residual heterogosity at single loci in homozygous androgenetic common carp (Cyprino carpio L.)

    NARCIS (Netherlands)

    Tanck, M.W.T.; Palstra, A.P.; Weerd, van de M.; Leffering, C.P.; Poel, van der J.J.; Bovenhuis, H.; Komen, J.

    2001-01-01

    Thirty-three androgenetic progeny groups of common carp were analysed using 11 microsatellite markers to (i) verify the homozygous status of the 566 androgenetic individuals, (ii) analyse the microsatellite allele segregation, and (iii) study the possible association of microsatellite alleles with p

  11. Microsatellite loci and the complete mitochondrial DNA sequence characterized through next generation sequencing and de novo genome assembly for the critically endangered orange-bellied parrot, Neophema chrysogaster.

    Science.gov (United States)

    Miller, Adam D; Good, Robert T; Coleman, Rhys A; Lancaster, Melanie L; Weeks, Andrew R

    2013-01-01

    A suite of polymorphic microsatellite markers and the complete mitochondrial genome sequence was developed by next generation sequencing (NGS) for the critically endangered orange-bellied parrot, Neophema chrysogaster. A total of 14 polymorphic loci were identified and characterized using DNA extractions representing 40 individuals from Melaleuca, Tasmania, sampled in 2002. We observed moderate genetic variation across most loci (mean number of alleles per locus = 2.79; mean expected heterozygosity = 0.53) with no evidence of individual loci deviating significantly from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. De novo and reference-based genome assemblies performed using MIRA were used to assemble the N. chrysogaster mitochondrial genome sequence with mean coverage of 116-fold (range 89 to 142-fold). The mitochondrial genome consists of 18,034 base pairs, and a typical metazoan mitochondrial gene content consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a single large non-coding region (control region). The arrangement of mitochondrial genes is also typical of Avian taxa. The annotation of the mitochondrial genome and the characterization of 14 microsatellite markers provide a valuable resource for future genetic monitoring of wild and captive N. chrysogaster populations. As found previously, NGS provides a rapid, low cost and reliable method for polymorphic nuclear genetic marker development and determining complete mitochondrial genome sequences when only a fraction of a genome is sequenced.

  12. Isolation and characterization of eight microsatellite loci from Galeocerdo cuvier (tiger shark) and cross-amplification in Carcharhinus leucas, Carcharhinus brevipinna, Carcharhinus plumbeus and Sphyrna lewini.

    Science.gov (United States)

    Pirog, Agathe; Jaquemet, Sébastien; Blaison, Antonin; Soria, Marc; Magalon, Hélène

    2016-01-01

    The tiger shark Galeocerdo cuvier (Carcharhinidae) is a large elasmobranch suspected to have, as other apex predators, a keystone function in marine ecosystems and is currently considered Near Threatened (Red list IUCN). Knowledge on its ecology, which is crucial to design proper conservation and management plans, is very scarce. Here we describe the isolation of eight polymorphic microsatellite loci using 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Their characteristics were tested on a population of tiger shark (n = 101) from Reunion Island (South-Western Indian Ocean). All loci were polymorphic with a number of alleles ranging from two to eight. No null alleles were detected and no linkage disequilibrium was detected after Bonferroni correction. Observed and expected heterozygosities ranged from 0.03 to 0.76 and from 0.03 to 0.77, respectively. No locus deviated from Hardy-Weinberg equilibrium and the global F IS of the population was of 0.04 (NS) . Some of the eight loci developed here successfully cross-amplified in the bull shark Carcharhinus leucas (one locus), the spinner shark Carcharhinus brevipinna (four loci), the sandbar shark Carcharhinus plumbeus (five loci) and the scalloped hammerhead shark Sphyrna lewini (two loci). We also designed primers to amplify and sequence a mitochondrial marker, the control region. We sequenced 862 bp and found a low genetic diversity, with four polymorphic sites, a haplotype diversity of 0.15 and a nucleotide diversity of 2 × 10(-4).

  13. Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz) Using Next-Generation Sequencing (NGS)

    Science.gov (United States)

    Bastías, Adriana; Correa, Francisco; Rojas, Pamela; Almada, Rubén; Muñoz, Carlos; Sagredo, Boris

    2016-01-01

    Maqui (Aristotelia chilensis [Molina] Stunz) is a small dioecious tree native to South America with edible fruit characterized by very high antioxidant capacity and anthocyanin content. To preserve maqui as a genetic resource it is essential to study its genetic diversity. However, the complete genome is unknown and only a few gene sequences are available in databases. Simple sequence repeats (SSR) markers, which are neutral, co-dominant, reproducible and highly variable, are desirable to support genetic studies in maqui populations. By means of identification and characterization of microsatellite loci from a maqui genotype, using 454 sequencing technology, we develop a set of SSR for this species. Obtaining a total of 165,043 shotgun genome sequences, with an average read length of 387 bases, we covered 64 Mb of the maqui genome. Reads were assembled into 4,832 contigs, while 98,546 reads remained as singletons, generating a total of 103,378 consensus genomic sequences. A total of 24,494 SSR maqui markers were identified. Of them, 15,950 SSR maqui markers were classified as perfects. The most common SSR motifs were dinucleotide (31%), followed by tetranucleotide (26%) and trinucleotide motifs (24%). The motif AG/CT (28.4%) was the most abundant, while the motif AC (89 bp) was the largest. Eleven polymorphic SSRs were selected and used to analyze a population of 40 maqui genotypes. Polymorphism information content (PIC) ranged from 0.117 to 0.82, with an average of 0.58. Non-significant groups were observed in the maqui population, showing a panmictic genetic structure. In addition, we also predicted 11150 putative genes and 3 microRNAs (miRNAs) in maqui sequences. This results, including partial sequences of genes, some miRNAs and SSR markers from high throughput next generation sequencing (NGS) of maqui genomic DNA, constitute the first platform to undertake genetic and molecular studies of this important species. PMID:27459734

  14. Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz Using Next-Generation Sequencing (NGS.

    Directory of Open Access Journals (Sweden)

    Adriana Bastías

    Full Text Available Maqui (Aristotelia chilensis [Molina] Stunz is a small dioecious tree native to South America with edible fruit characterized by very high antioxidant capacity and anthocyanin content. To preserve maqui as a genetic resource it is essential to study its genetic diversity. However, the complete genome is unknown and only a few gene sequences are available in databases. Simple sequence repeats (SSR markers, which are neutral, co-dominant, reproducible and highly variable, are desirable to support genetic studies in maqui populations. By means of identification and characterization of microsatellite loci from a maqui genotype, using 454 sequencing technology, we develop a set of SSR for this species. Obtaining a total of 165,043 shotgun genome sequences, with an average read length of 387 bases, we covered 64 Mb of the maqui genome. Reads were assembled into 4,832 contigs, while 98,546 reads remained as singletons, generating a total of 103,378 consensus genomic sequences. A total of 24,494 SSR maqui markers were identified. Of them, 15,950 SSR maqui markers were classified as perfects. The most common SSR motifs were dinucleotide (31%, followed by tetranucleotide (26% and trinucleotide motifs (24%. The motif AG/CT (28.4% was the most abundant, while the motif AC (89 bp was the largest. Eleven polymorphic SSRs were selected and used to analyze a population of 40 maqui genotypes. Polymorphism information content (PIC ranged from 0.117 to 0.82, with an average of 0.58. Non-significant groups were observed in the maqui population, showing a panmictic genetic structure. In addition, we also predicted 11150 putative genes and 3 microRNAs (miRNAs in maqui sequences. This results, including partial sequences of genes, some miRNAs and SSR markers from high throughput next generation sequencing (NGS of maqui genomic DNA, constitute the first platform to undertake genetic and molecular studies of this important species.

  15. Isolation and Characterization of Microsatellite Loci for Hibiscus aridicola (Malvaceae, an Endangered Plant Endemic to the Dry-Hot Valleys of Jinsha River in Southwest China

    Directory of Open Access Journals (Sweden)

    Kaiyun Guan

    2011-09-01

    Full Text Available Hibiscus aridicola (Malvaceae is an endangered ornamental shrub endemic to the dry-hot valleys of Jinsha River in southwest China. Only four natural populations of H. aridicola exist in the wild according to our field investigation. It can be inferred that H. aridicola is facing a very high risk of extinction in the wild and an urgent conservation strategy is required. By using a modified biotin-streptavidin capture method, a total of 40 microsatellite markers were developed and characterized in H. aridicola for the first time. Polymorphisms were evaluated in 39 individuals from four natural populations. Fifteen of the markers showed polymorphisms with two to six alleles per locus; the observed heterozygosity ranged from 0.19 to 0.72. These microsatellite loci would be useful tools for population genetics studies on H. aridicola and other con-generic species which are important to the conservation and development of endangered species.

  16. Identification and characterization of polymorphic microsatellite loci in the blue shark Prionace glauca, and cross-amplification in other shark species.

    Science.gov (United States)

    Mendonça, F F; Ussami, L H F; Hashimoto, D T; Pereira, L H G; Porto-Foresti, F; Oliveira, C; Gadig, O B F; Foresti, F

    2012-06-01

    Two to 14 alleles were found to be segregating per locus (mean 5·2), with observed and expected heterozygosities ranging from 0·08 to 0·78 and 0·08 to 0·94, respectively. Cross-amplification of six of these microsatellite loci indicated that they are also polymorphic in three species of Carcharhiniformes and two species of Lamniformes. The newly developed primers reported here constitute a useful tool for genetic population analyses on Prionace glauca and, potentially, other related species. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

  17. Utilizing next generation sequencing to characterize microsatellite loci in a tropical aquatic plant species Cryptocoryne cordata var. cordata (Araceae)

    DEFF Research Database (Denmark)

    Rosazlina, Rusly; Jacobsen, Niels; Ørgaard, Marian

    2015-01-01

    designed and tested for efficiency in polymerase chain reaction amplification. Using these primer sets, 11 new microsatellite marker loci were successfully amplified with unambiguous polymorphic alleles exhibited across 30 individuals examined. The number of alleles per locus ranged from 2 to 6, while...... for the species using next generation sequencing (Roche 454 pyrosequencing) from genomic DNA. A total of 41,653 reads was generated, of which 3636 fragments contained at least one repeat motif. Seventy two primer sets in the flanking region of dinucleotide, trinucleotide and tetranucleotides repeat motifs were...

  18. A wheat intervarietal genetic linkage map based on microsatellite and target region amplified polymorphism markers and its utility for detecting quantitative trait loci.

    Science.gov (United States)

    Liu, Z H; Anderson, J A; Hu, J; Friesen, T L; Rasmussen, J B; Faris, J D

    2005-08-01

    Efficient user-friendly methods for mapping plant genomes are highly desirable for the identification of quantitative trait loci (QTLs), genotypic profiling, genomic studies, and marker-assisted selection. SSR (microsatellite) markers are user-friendly and efficient in detecting polymorphism, but they detect few loci. Target region amplification polymorphism (TRAP) is a relatively new PCR-based technique that detects a large number of loci from a single reaction without extensive pre-PCR processing of samples. In the investigation reported here, we used both SSRs and TRAPs to generate over 700 markers for the construction of a genetic linkage map in a hard red spring wheat intervarietal recombinant inbred population. A framework map consisting of 352 markers accounted for 3,045 cM with an average density of one marker per 8.7 cM. On average, SSRs detected 1.9 polymorphic loci per reaction, while TRAPs detected 24. Both marker systems were suitable for assigning linkage groups to chromosomes using wheat aneuploid stocks. We demonstrated the utility of the maps by identifying major QTLs for days to heading and reduced plant height on chromosomes 5A and 4B, respectively. Our results indicate that TRAPs are highly efficient for genetic mapping in wheat. The maps developed will be useful for the identification of quality and disease resistance QTLs that segregate in this population.

  19. Long-tailed Duck (Clangula hyemalis) Microsatellite DNA Data; Alaska, Canada, Russia, 1994-2002

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This data set describes nuclear microsatellite genotypes derived from twelve autosomal loci (6AB, Aph02, Aph08, Aph19, Aph23, Bca10, Bca11, Hhi5, Sfi11, Smo07,...

  20. Monomorphic Analysis of Microsatellite Loci at BAT-26%微卫星BAT-26位点单态性的分析

    Institute of Scientific and Technical Information of China (English)

    狄金明; 张一楚; 陈蕾; 顾琴龙

    2001-01-01

    Objective MSI plays an important role in carainogenesis of manttumors.Most MS loci show polymorphism in normal tissues.It has been reported that BAT-26 was quasi-monomorphic,showing only minor size variathions.To analysis monomorphism at BAT-26 loci,60 normal colorectal tissues were examined.Methods Genomic DNA extracted from tissues was PCR amplified.PCR products were run on 6% denaturing polyacrylamide gel and stained with silver.Results All specimens showed no variation in the length of MS DNA at BAT-26 loci.Conclusion BAT-26 has much monomorphism in human genome.%目的 微卫星不稳定性(MicrosatelliteInstability,MSI)在许多肿瘤的发生中具很重要的作用,大多数微卫星(Microsatellite,MS)位点在正常人群中多态性明显,有报道表明BAT-26位点单态性很好,据此我们分析了60例正常肠粘膜标本中BAT-26位点MSDNA的情况,以便了解BAT-26位点单态性情况。方法 组织DNA提取后PCR扩增,扩增产物行6%变性聚丙烯酰胺凝胶电泳,最后银染。结果 所有标本在BAT-26位点MSDNA长度无明显改变。结论 BAT-26具有较好的单态性。

  1. DNA microsatellite characterization of the jaguar (Panthera onca) in Colombia.

    Science.gov (United States)

    Ruiz-Garcia, Manuel; Payán, Esteban; Murillo, Andrea; Alvarez, Diana

    2006-04-01

    The Colombian jaguar population is thought to contain two different subspecies, Panthera onca centralis and Panthera onca onca. The genetic structure of this population was evaluated using 12 microsatellite loci (n = 62 samples). In addition, 22 jaguar DNA samples from Guatemala, Paraguay, Perú, Bolivia, Venezuela and Brazil were analyzed for these microsatellite loci (n = 84 samples). The results of this study indicate six primary themes. First, the levels of gene diversity were very high. Second, the majority of the loci analyzed showed an absence of Hardy-Weinberg equilibrium, probably due to the Wahlund effect (= population subdivision). Third, several microsatellite loci showed significant heterogeneity between the two supposed subspecies in the country. Nevertheless, gene flow was present between them, and heterogeneity was relatively low, although the assignment analyses showed good classification of the jaguars studied into their respective subspecies. Fourth, the long-term historical effective population sizes were calculated through a maximum likelihood procedure for single and multi-step mutation models. Fifth, seven out of twelve DNA microsatellites studied significantly deviated from a single-step mutation model. However, the overall mean multi-step mutation percentage for these 12 DNA microsatellites was only 6%. Therefore, 94% of mutations were uni-step. Sixth, no bottleneck events were detected in the Colombian jaguar population overall.

  2. Characterization of twelve novel microsatellite markers of Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) identified from next generation sequence data

    Science.gov (United States)

    The white-backed planthopper, Sogatella furcifera (Horváth) (Hemiptera: Delphacidae), is a major pest of rice and has long-range migratory behavior in Asia. Microsatellite markers (simple sequence repeats, SSRs) have been widely used to determine the origins and genetic diversity of insect pests. ...

  3. Isolation and characterization of 21 microsatellite loci in Cardiocrinum giganteum var. yunnanense (Liliaceae), an important economic plant in China.

    Science.gov (United States)

    Li, Rong; Yang, Jie; Yang, Junbo; Dao, Zhiling

    2012-01-01

    Twenty-one microsatellite markers from the genome of Cardiocrinum giganteum var. yunnanense, an important economic plant in China, were developed with a fast isolation protocol by amplified fragment length polymorphism of sequences containing repeats (FIASCO). Polymorphism within each locus was assessed in 24 wild individuals from Gaoligong Mountains in western Yunnan Province, China. The number of alleles per locus ranged from 2 to 4 with a mean of 2.9. The expected and observed levels of heterozygosity ranged from 0.042 to 0.726 and from 0.000 to 1.000, with averages of 0.44 and 0.31, respectively. These polymorphic microsatellite markers should prove useful in population genetics studies and assessments of genetic variation to develop conservation and management strategies for this species.

  4. Isolation, characterization and PCR multiplexing of microsatellite loci for two sub-species of terrestrial isopod Porcellio dilatatus (Crustacea, Oniscidea).

    Science.gov (United States)

    Michaud, Caroline; Chupeau, Cassandre; Bech, Nicolas; Thierry, Magali; Sicard, Mathieu; Greve, Pierre; Beltran-Bech, Sophie

    2016-04-01

    Several microsatellite markers have already been developed for different terrestrial isopod species such as Armadillidium vulgare, A. nasatum and Porcellionides pruinosus. In all these species, the endosymbiont Wolbachia has a feminizing effect that generates a female bias in sex ratio and reduces the number of reproductive males. Thus this can potentially decrease the genetic diversity of host populations. However, in some other isopod species, Wolbachia induces cytoplasmic incompatibility (CI); the most commonly described effect of Wolbachia in arthropods. The CI by rendering some crossings incompatible can reduce the gene flow and strengthen genetic differentiation between isopod populations. To date, the influence of Wolbachia inducing CI on population structure of terrestrial isopods has never been investigated. In this study, we developed 10 polymorphic microsatellite markers shared by two sub-species of Porcellio dilatatus. Crossings between the two sub-species are partially incompatible due to two CI-inducing Wolbachia strains. These new microsatellite markers will allow us to investigate the effect of CI on host genetic differentiation in this species complex.

  5. Genetic variability and forensic efficiency of 39 microsatellite loci in the Li ethnic group from Hainan Island in the South China Sea.

    Science.gov (United States)

    Chen, Jing; Xie, Bingbing; Yang, Yaran; Yang, Meng; Liu, Chao; Lv, Yuexin; Chen, Chuguang; Liu, Xu; Fang, Xiangdong; Wu, Huijuan; Yan, Jiangwei

    2017-08-01

    Investigation of allele and genotype frequencies of microsatellite loci in various populations is an essential pre-requisite in forensic application. The present study obtained population genetic data and forensic parameters of 39 autosomal Short Tandem Repeats (STRs) loci from a Chinese Li ethnic group and estimated the genetic relationships between Li and other reference populations. Thirty-nine STR loci, which include D19S433, D5S818, D21S11, D18S51, D6S1043, D3S1358, D13S317, D7S820, D16S539, CSF1PO, Penta D, D2S441, vWA, D8S1179, TPOX, Penta E, TH01, D12S391, D2S1338, FGA, D6S477, D18S535, D19S253, D15S659, D11S2368, D20S470, D1S1656, D22-GATA198B05, D8S1132, D4S2366, D21S1270, D13S325, D9S925, D3S3045, D14S608, D10S1435, D7S3048, D17S1290 and D5S2500, were amplified in two multiplex DNA-STR fluorescence detection systems for 189 unrelated healthy individuals of the Chinese Li ethnic group. The allele frequency distribution and several parameters commonly used in forensic science were statistically analysed. A total of 378 alleles were observed with corresponding allelic frequencies ranging from 0.0026-0.5899. The power of discrimination and power of exclusion ranged from 0.7569-0.9672 and 0.2513-0.7355, respectively. The power of exclusion (PE) ranged from 0.2580-0.7943 for trio paternity cases and 0.1693-0.5940 for duo paternity cases. The polymorphism information content (PIC) ranged from 0.5001-0.8611. The cumulative match probability across these 39 loci was 2.4242 × 10(-38). The results indicate that 39 STR loci are polymorphic among the Li ethnic group in Hainan Island in the South China Sea. This set of polymorphic STR loci provide highly polymorphic information and forensic efficiency for forensic individual identification and paternity testing, as well as basic population data for population genetics and anthropological research.

  6. Development and characterisation of 20 microsatellite loci isolated from the large bent-wing bat, Miniopterus schreibersii (Chiroptera: Miniopteridae) and their cross-taxa utility in the family Miniopteridae.

    Science.gov (United States)

    Wood, Rebecca; Weyeneth, Nicole; Appleton, Belinda

    2011-07-01

    The large bent-wing bat, Miniopterus schreibersii (Kuhl 1819), has a long history of taxonomic uncertainty and many populations are known to be in a state of decline. Microsatellite loci were developed for the taxonomic and population genetic assessment of the Australian complex of this species. Of the 33 primer sets designed for this research, seven (21%) were deemed suitably polymorphic for population-level analyses of the Australian taxa, with five (71%) of these loci revealing moderate to high levels of polymorphism (PIC = 0.56 to 0.91). The cross-taxa utility of the M. schreibersii microsatellite markers was assessed in the microbat (Chiroptera) family Miniopteridae. Sub-species and species covering the Miniopteridae's global distribution (with the exception of the Middle East) were selected, numbering 25 taxa in total. Amplification was successful for 26 loci, of which 20 (77%) were polymorphic. High cross-taxa utility of markers was observed with amplification achieved for all taxa for between four (20%) and 20 (100%) loci, and polymorphism was considered moderate to high (PIC = 0.47-0.91) for 12 (60%) of these loci. The high cross-taxa utility of the microsatellites reported herein reveal versatile and cost-effective molecular markers, contributing an important genetic resource for the research and conservation of Miniopteridae species worldwide.

  7. Genetic Diversity in Four Microsatellite Loci BMS1915, BMS1350, LGB and ILSTS45 in Baluchi Sheep

    Directory of Open Access Journals (Sweden)

    R. Valizadeh

    2013-08-01

    Full Text Available The poly morphism of 4 micro satellite loci (BMS1350, LGB, ILSTS45, BMS1915 associated with functional traits were evaluated for detecting the diversity level in Baluchi breed of sheep. One hundred eighty five blood samples were collected from sheep herd in Abbas-Abad breeding station. DNA extraction was performed using guanidinethiocyanate silica gel method. Gene fragments of micro satellites were amplified by polymerase chain reaction based on the recommended standard method. The PCR products were visible using poly acry lamide gel electrophoresis and stain methods with silver. Alleles were typed using the Photocapt software version 3. All loci were in the Hardy-Weinberg equilibrium (p

  8. Isolation and characterization of microsatellite loci in Sorbus porrigentiformis and cross-amplification in S. aria and S. rupicola (Rosaceae)1

    Science.gov (United States)

    Piñeiro, Rosalía; Karrman-Bailey, Freja; Cowan, Robyn S.; Fay, Michael F.

    2017-01-01

    Premise of the study: Southwestern Britain is an emblematic hotspot of polyploid diversity of whitebeams (Sorbus aria agg.; Rosaceae) with ca. 30 polyploid endemic species. The tetraploid S. porrigentiformis is postulated as one of the parents of most of these endemics, along with the sexual diploid S. aria s. str. and the tetraploid S. rupicola. Methods and Results: We isolated 16 nuclear microsatellite loci from S. porrigentiformis and characterized them on 45 trees representing the three putative parental species. Eleven loci were polymorphic, and eight of them exhibited species-specific alleles. Allele numbers ranged from one to 11, and observed heterozygosity ranged from 0.40 to 1.00. The intraspecific levels of variation were very low, in agreement with the facultative apomictic reproduction hypothesized for this species. Conclusions: The species-specific alleles will be useful for tracing the origin of the narrowly distributed Sorbus taxa. In addition, the assessment of diversity levels will help design a conservation strategy for the polyploid complex. PMID:28224061

  9. Development and cross-species amplification of microsatellite loci for Puccinellia maritima, an important engineer saltmarsh species.

    Science.gov (United States)

    Rouger, R; Vallejo-Marin, M; Jump, A S

    2014-04-30

    The grass Puccinellia maritima is an important saltmarsh ecosystem engineer exhibiting wide morphological variation, which is partially genetically determined. Nevertheless, nothing is known about its population genetics or how neutral genetic variation is distributed throughout its geographical range. Here, we describe 12 polymorphic microsatellites pooled into two multiplexes for this octoploid species. Assessment of 24 samples from three populations revealed 4 to 29 alleles per locus, with variation in allele presence and abundance between populations. The transferability of these markers is reported based on their cross-amplification in six other Puccinellia species of different ploidy levels.

  10. Population structure of African buffalo inferred from mtDNA sequences and microsatellite loci: high variation but low differentiation

    DEFF Research Database (Denmark)

    Simonsen, Bo Thisted; Siegismund, H R; Arctander, P

    1998-01-01

    The African buffalo (Syncerus caffer) is widespread throughout sub-Saharan Africa and is found in most major vegetation types, wherever permanent sources of water are available, making it physically able to disperse through a wide range of habitats. Despite this, the buffalo has been assumed...... of mtDNA and microsatellite data were found to be congruent, disagreeing with the alleged male-biased dispersal. We propose that the observed pattern of the distribution of genetic variation between buffalo populations at the regional level can be caused by fragmentation of a previous panmictic...

  11. 柑橘全爪螨微卫星位点鉴定与信息分析%Analysis of Microsatellite Loci fromPanonychus citri Based on Enriched Microsatellite Library and Transcriptome Dataset

    Institute of Scientific and Technical Information of China (English)

    魏丹丹; 刘燕; 杜洋; 李刚; 李婷; 袁明龙; 王进军

    2016-01-01

    , msatcommander software and bioinformatics methods were used to identify and assess of the quality and quantity of EST-SSR loci from P. citritranscriptome dataset. Primer Premier 5 was used to designP. citriSSR primers, and then these primer pairs were verified by PCR.[Result]Three microsatellite-enriched libraries of AC-repeat, TC-repeat, and ATG-repeat were constructed forP. citri. The positive clone rates of these three libraries were about 30%, 28% and 25%, respectively. The sequencing results showed that the AC library had the highest redundancy rate, and the TC library followed. However, the same clone of SSR in the ATG library was not found. Intriguingly, in the AC library, some AC-repeat types of SSRs existed in many copies with similar or almost identical sequences in one of the flanking regions. Totally, 44 unique microsatellite loci (GenBank number JF776418-JF776461) were obtained. Among these SSRs, 20 primer pairs were synthesized, and 11 primer pairs could be steadily amplified. In gSSR, perfect SSR accounted for 54.5%, and imperfect perfected and compound SSR accounted for 27.3% and 18.2%, respectively. In perfect gSSR, the repeat times (13-42 times) of the di-nucleotide repeat SSR were much higher than tri-nucleotide repeat SSR (5-9 times). A total of 8 023 EST-SSR loci were identified fromP. citri transcriptome, and 2 540 SSR sequences could be used for primer design. A total of 35 primer pairs were synthesized (GenBank number KT261306-KT261340), and 8 primer pairs could be steadily amplified. The average distribution distance of the transcriptomic SSRs was 3.55 kb. Tri-nucleotide repeat SSR was the most frequently occurring type in P. citri EST-SSR (53.86%), and di-nucleotide repeat SSR was followed (43.36%). The tetra-, penta-, hexa- nucleotide repeat and compound SSR were very scarce with similar numbers, and accounted for 2.78% in total. The repeat of times of the EST-SSR motifs were mainly concentrated in 5-10 times.[Conclusion]Microsatellite enrichment by

  12. Development of Nine Markers and Characterization of the Microsatellite Loci in the Endangered Gymnogobius isaza (Gobiidae

    Directory of Open Access Journals (Sweden)

    Hiroshi Kudoh

    2012-05-01

    Full Text Available Gymnogobius isaza is a freshwater goby endemic to Lake Biwa, Japan. They experienced a drastic demographic bottleneck in the 1950s and 1980s and slightly recovered thereafter, but the population size is still very small. To reveal dynamics of genetic diversity of G. isaza, we developed nine microsatellite markers based on the sequence data of a related goby Chaenogobius annularis. Nine SSR (Simple Sequence Repeats markers were successfully amplified for raw and formalin-fixed fish samples. The number of alleles and expected heterozygosities ranged from one to 10 and from 0.06 to 0.84, respectively, for the current samples, while one to 12 and 0.09 to 0.83 for historical samples. The markers described here will be useful for investigating the genetic diversity and gene flow and for conservation of G. isaza.

  13. Population genetic structure of the blue-fronted Amazon (Amazona aestiva, Psittacidae: Aves) based on nuclear microsatellite loci: implications for conservation.

    Science.gov (United States)

    Leite, K C E; Seixas, G H F; Berkunsky, I; Collevatti, R G; Caparroz, R

    2008-09-09

    The blue-fronted Amazon (Amazona aestiva) is a widely distributed Neotropical parrot and one of the most captured parrots in nature to supply the illegal trade of wild animals. The objectives of the present study were to analyze the genetic structure of A. aestiva to identify management units and support conservation planning and to verified if A. aestiva populations have undergone a recent bottleneck due to habitat loss and capture for the pet trade. The genetic structure was accessed by analyzing six microsatellite loci in 74 individuals of A. aestiva, including samples from the two subspecies (A. a. aestiva and A. a. xanthopteryx), from five populations: four in Brazil and one in Argentina. A significant genetic differentiation (theta = 0.007, p = 0.005) could be detected only between the most distant populations, Tocantins and Argentina, localized at the northeast and southwest limits of the sample sites, respectively. There was no evidence of inbreeding within or between populations, suggesting random mating among individuals. These results suggest a clinal distribution of genetic variability, as observed for variation in plumage color of the two A. aestiva subspecies. Bottleneck analysis did not show a recent reduction in population size. Thus, for the management and conservation of the species, the populations from Argentina and Tocantins should be considered as different management units, and the other populations from the center of the geographical distribution as another management unit.

  14. Development and characterization of 12 microsatellite markers for the Island Night Lizard (Xantusia riversiana), a threatened species endemic to the Channel Islands, California, USA

    Science.gov (United States)

    O'Donnell, Ryan P.; Drost, Charles A.; Mock, Karen E.

    2014-01-01

    The Island Night Lizard is a federally threatened species endemic to the Channel Islands of California. Twelve microsatellite loci were developed for use in this species and screened in 197 individuals from across San Nicolas Island, California. The number of alleles per locus ranged from 6 to 21. Observed heterozygosities ranged from 0.520 to 0.843. These microsatellite loci will be used to investigate population structure, effective population size, and gene flow across the island, to inform protection and management of this species.

  15. Development and characterization of microsatellite markers for Piptadenia gonoacantha (Fabaceae)1

    Science.gov (United States)

    Grando, Carolina; Bajay, Miklos M.; Bajay, Stephanie K.; Schwarcz, Kaiser D.; Campos, Jaqueline B.; Brancalion, Pedro H. S.; Pinheiro, José B.; Rodrigues, Ricardo R.; Souza, Anete P.; Zucchi, Maria I.

    2015-01-01

    • Premise of the study: Microsatellite primers were designed for Piptadenia gonoacantha (Fabaceae) and characterized to estimate genetic diversity parameters. The species is a native tree from the Atlantic Forest biome commonly used in forest restoration; it has medicinal potential and the wood is economically useful. • Methods and Results: Twenty-eight microsatellite loci were identified from an enriched genomic library. Fifteen loci resulted in successful amplifications and were characterized in a natural population of 94 individuals. Twelve loci were polymorphic, with allele numbers ranging from three to 15 per locus, and expected and observed heterozygosities ranging from 0.2142 to 0.8325 and 0.190 to 0.769, respectively. • Conclusions: The developed markers will be used in further studies of population genetics of P. gonoacantha, aimed at conservation and management of the species in natural populations and in forest restoration projects. PMID:25699220

  16. Genetic characterization of 12 heterologous microsatellite markers for the giant tropical tree Cariniana legalis (Lecythidaceae

    Directory of Open Access Journals (Sweden)

    Marcela Corbo Guidugli

    2010-01-01

    Full Text Available Twelve microsatellite loci previously developed in the tropical tree Cariniana estrellensis were genetically characterized in Cariniana legalis. Polymorphisms were assessed in 28 C. legalis individuals found between the Pardo and Mogi-Guaçu River basins in the state of São Paulo, Brazil. Of the 12 loci, 10 were polymorphic and exhibited Mendelian inheritance. The allelic richness at each locus ranged from 2-11, with an average of 7 alleles per locus, and the expected heterozygosity ranged from 0.07-0.88. These loci showed a high probability of paternity exclusion. The characteristics of these heterologous microsatellite markers indicate that they are suitable tools for investigating questions concerning population genetics in C. legalis.

  17. Genetic structure of African buffalo herds based on variation at the mitochondrial D-loop and autosomal microsatellite loci: Evidence for male-biased gene flow

    NARCIS (Netherlands)

    Hooft, van W.F.; Groen, A.F.; Prins, H.H.T.

    2003-01-01

    Sexual differences in herding behaviour of African buffalo (Syncerus caffer) were studied by analysing at the herd level mitochondrial D-loop hypervariable region I and fourteen autosomal microsatellites. Three herds from Arusha National Park in Tanzania were analysed with mtDNA and five herds from

  18. A linkage map of cultivated cucumber (cucumis sativus l.) with 248 microsatellite marker loci and seven genes for horticulturally important traits

    Science.gov (United States)

    Marker assisted selection (MAS) is playing an increasingly important role in expedite and increase the efficiency of classical plant breeding. In cucumber, MAS is lagging behind as compared with other field crops. In the present study, a genetic map was developed with microsatellite (or simple seque...

  19. Population genetic structure of Siniperca chuatsi in the middle reach of the Yangtze River inferred from mitochondrial DNA and microsatellite loci.

    Science.gov (United States)

    Tian, Changxu; Yang, Min; Liang, Xu-Fang; Cao, Liang; Zheng, Hezi; Zhao, Cheng; Zhu, Kecheng; Yuan, Yongchao

    2015-02-01

    The Chinese mandarin fish (Siniperca chuatsi) is currently one of the most important economic freshwater fish in China, whereas the wild resource has declined dramatically in recent years. In this study, we examined the genetic structure and diversity of five populations from the middle reach of the Yangtze River using mitochondrial cytochrome b sequences and microsatellite markers. This research revealed high genetic diversity and low genetic differentiation of S. chuatsi from these regions. The pairwise Fst values of the two markers showed low and no-significant differentiation among populations. AMOVA analysis of two markers and the haplotype genealogy of the Cytb gene confirmed these results. The STRUCTURE analysis of the microsatellite marker implied that the dam upon the tributary of the Yangtze River blocked the gene flow among those regions. This research will be useful in breeding programs and conservation management of this species.

  20. Microsatellite instability in bladder cancer

    DEFF Research Database (Denmark)

    Gonzalez-Zulueta, M; Ruppert, J M; Tokino, K;

    1993-01-01

    Somatic instability at microsatellite repeats was detected in 6 of 200 transitional cell carcinomas of the bladder. Instabilities were apparent as changes in (GT)n repeat lengths on human chromosome 9 for four tumors and as alterations in a (CAG)n repeat in the androgen receptor gene on the X...... chromosome for three tumors. Single locus alterations were detected in three tumors, while three other tumors revealed changes in two or more loci. In one tumor we found microsatellite instability in all five loci analyzed on chromosome 9. The alterations detected were either minor 2-base pair changes...

  1. Nuclear microsatellite primers for the endangered relict fir, Abies pinsapo (Pinaceae) and cross-amplification in related Mediterranean Species.

    Science.gov (United States)

    Sánchez-Robles, Jose M; Balao, Francisco; García-Castaño, Juan L; Terrab, Anass; Navarro-Sampedro, Laura; Talavera, Salvador

    2012-11-05

    Twelve nuclear microsatellite primers (nSSR) were developed for the endangered species Abies pinsapo Boiss. to enable the study of gene flow and genetic structure in the remaining distribution areas. Microsatellite primers were developed using next-generation sequencing (454) data from a single Abies pinsapo individual. Primers were applied to thirty individuals from the three extant localities. The number of alleles per locus ranged from one to four. Cross-amplification was tested for other Abies species from the Mediterranean Basin, and most of the loci showed higher polymorphisms in the Mediterranean species than in A. pinsapo. These microsatellite markers provide tools for conservation genetic studies in Abies pinsapo as well other Abies species from the Mediterranean Basin.

  2. Nuclear Microsatellite Primers for the Endangered Relict Fir, Abies pinsapo (Pinaceae and Cross-Amplification in Related Mediterranean Species

    Directory of Open Access Journals (Sweden)

    Laura Navarro-Sampedro

    2012-11-01

    Full Text Available Twelve nuclear microsatellite primers (nSSR were developed for the endangered species Abies pinsapo Boiss. to enable the study of gene flow and genetic structure in the remaining distribution areas. Microsatellite primers were developed using next-generation sequencing (454 data from a single Abies pinsapo individual. Primers were applied to thirty individuals from the three extant localities. The number of alleles per locus ranged from one to four. Cross-amplification was tested for other Abies species from the Mediterranean Basin, and most of the loci showed higher polymorphisms in the Mediterranean species than in A. pinsapo. These microsatellite markers provide tools for conservation genetic studies in Abies pinsapo as well other Abies species from the Mediterranean Basin.

  3. HMSRP Hawaiian Monk Seal Microsatellite Genotypes

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Currently ~2,400 Hawaiian monk seal specimens have been analyzed genetically, providing genotypes at 18 microsatellite loci. These data are organized by individual,...

  4. Fine genetic mapping of the Batten disease locus (CLN3) by haplotype analysis and demonstration of allelic association with chromosome 16p microsatellite loci

    Energy Technology Data Exchange (ETDEWEB)

    Mitchison, H.M.; McKay, T.R. [Univ. College London Medical School (United Kingdom); Thompson, A.D.; Mulley, J.C.; Kozman, H.M.; Richards, R.I.; Callen, D.F. [Women and Children`s Hospital, Adelaide (Australia); Stallings, R.L.; Doggett, N.A. [Los Alamos National Lab., NM (United States); Attwood, J. [Galton Lab., London (United Kingdom)] [and others

    1993-05-01

    Batten disease, juvenile onset neuronal ceroid lipofuscinosis, is an autosomal recessive neurodegenerative disorder characterized by accumulation of autofluorescent lipopigment in neurons and other cell types. The disease locus (CLN3) has previously been assigned to chromosome 16p. The genetic localization of CLN3 has been refined by analyzing 70 families using a high-resolution map of 15 marker loci encompassing the CLN3 region on 16p. Crossovers in three maternal meioses allowed localization of CLN3 to the interval between D16S297 and D16S57. Within that interval alleles at three highly polymorphic dinucleotide repeat loci (D16S288, D16S298, D16S299) were found to be in strong linkage disequilibrium with CLN3. Analysis of haplotypes suggests that a majority of CLN3 chromosomes have arisen from a single founder mutation. 15 refs., 2 figs., 5 tabs.

  5. RAPD identification of microsatellites in Daphnia

    NARCIS (Netherlands)

    Ender, A.; Schwenk, K.; Stadler, T.; Streit, B.; Schierwater, B.

    1996-01-01

    Simple sequence repeats (SSRs, or microsatellites) have been constantly gaining importance as single-locus DNA markers in population genetics and behavioural ecology. We tested a PCR- based strategy for finding microsatellite loci in anonymous genomes, which avoids genomic library construction and s

  6. NEW MICROSATELLITE LOCI IN THE MUD CRAB SCYLLA PARAMAMOSAIN DEVELOPED BY HYBRIDIZATION TO (AG)12 BIOTIN-LABELED PROBE%拟穴青蟹(Scylla paramamosain)微卫星位点开发——基于(AG)12探针杂交

    Institute of Scientific and Technical Information of China (English)

    宋忠魁; 聂振平; 谢达; 王芳宇

    2013-01-01

    FIASCO (Fast Isolation by AFLP Sequences Containing repeats) technique and magnetic bead enrichment method were used to develop microsatellite loci of the mud crab Scylla paramamosain. The results showed that more mi-crosatellite sequences distributed within the range of 400bp in length and the probabilities of perfect microsatellite increased from di- to pentamer repeated types. 28 primer pairs were designed to amplify a sampling population, while 12 polymorphic loci were amplified, whose length conformed to theory size basically. Ten loci displayed polymorphic highly and nine loci were deviated from Hardy-Weinberg equilibrium (HWE) significantly (P<0.05). Significant linkage disequilibrium was detected in two pairwise loci (P<0.0042, corrected by Bonferroni method). Micro-Checker analysis suggested that five loci were involved in PCR amplification of null alleles. Regardless of the primer pairs of microsatellite mixture (containing two microsatellite sites or more), plus some loci with PIC value lower than 0.5, eight primer pairs proved useful for the related population genetic analysis.%采用FIASCO (Fast Isolation by AFLP Sequences Containing repeats)技术和磁珠富集方法开发拟穴青蟹微卫星位点.结果表明,400bp以下长度的序列含微卫星的概率超过400bp以上长度的序列;从二碱基重复类型到五碱基重复类型,完美型微卫星的概率在增加.利用设计的28对引物扩增一个供试群体,其中12对引物能稳定扩增且片段大小基本符合理论长度,10个微卫星位点表现出高度多态性,9个微卫星位点显著偏离Hardy-Weinberg平衡(P<0.05),两组两两位点间存在连锁不平衡现象(P<0.0042,经Bonferroni法校正).Micro-Checker分析揭示其中的5个微卫星位点可能存在无效等位基因.排除混合微卫星位点的引物对以及扩增位点PIC值在0.5以下的引物对,8对引物能用于拟穴青蟹群体遗传学等研究.

  7. Application of Novel Polymorphic Microsatellite Loci Identified in the Korean Pacific Abalone (Haliotis diversicolor supertexta (Haliotidae in the Genetic Characterization of Wild and Released Populations

    Directory of Open Access Journals (Sweden)

    Seong Wan Hong

    2012-08-01

    Full Text Available The small abalone, Haliotis diversicolor supertexta, of the family Haliotidae, is one of the most important species of marine shellfish in eastern Asia. Over the past few decades, this species has drastically declined in Korea. Thus, hatchery-bred seeds have been released into natural coastal areas to compensate for the reduced fishery resources. However, information on the genetic background of the small abalone is scarce. In this study, 20 polymorphic microsatellite DNA markers were identified using next-generation sequencing techniques and used to compare allelic variation between wild and released abalone populations in Korea. Using high-throughput genomic sequencing, a total of 1516 (2.26%; average length of 385 bp reads containing simple sequence repeats were obtained from 86,011 raw reads. Among the 99 loci screened, 28 amplified successfully, and 20 were polymorphic. When comparing allelic variation between wild and released abalone populations, a total of 243 different alleles were observed, with 18.7 alleles per locus. High genetic diversity (mean heterozygosity = 0.81; mean allelic number = 15.5 was observed in both populations. A statistical analysis of the fixation index (FST and analysis of molecular variance (AMOVA indicated limited genetic differences between the two populations (FST = 0.002, p > 0.05. Although no significant reductions in the genetic diversity were found in the released population compared with the wild population (p > 0.05, the genetic diversity parameters revealed that the seeds released for stock abundance had a different genetic composition. These differences are likely a result of hatchery selection and inbreeding. Additionally, all the primer pair sets were effectively amplified in another congeneric species, H. diversicolor diversicolor, indicating that these primers are useful for both abalone species. These microsatellite loci

  8. Genome evolution trend of common carp (Cyprinus carpio L.) as revealed by the analysis of microsatellite loci in a gynogentic family

    Institute of Scientific and Technical Information of China (English)

    Yan Zhang; Liqun Liang; Peng Jiang; Dayu Li; Cuiyun Lu; Xiaowen Sun

    2008-01-01

    Genome evolution arises from two main ways of duplication and reduction. Fish specific genome duplication (FSGD) may have oc curred before the radiation of the teleosts. Common carp {Cyprinus carpio L.) has been considered to be a tetraploid species, because of its chromosome numbers (2n=100) and its high DNA content. Using 69 microsatellite primer pairs, the variations were studied to better understand the genome evolution (genome duplication and diploidization) of common carp from a gynogenetic family. About 48% of primer pairs were estimated to amplify duplicates based on the number of PCR amplification per individual. Segregation patterns in the family suggested a partially duplicated genome structure and disomic inheritance. This indicates that the common carp is tetraploid and polyploidy occurred by allotetraploidy. Two primer pairs (HLJ021 and HLJ332) were estimated to amplify reduction based on the number of PCR amplification per individual. One allele in HLJ002 locus and HLJ332 locus was clearly lost in the gynogenetic family and the same as in six wild populations. Segregation patterns in the family suggested a partially diplodization genome structure. A hypothesis transition (dynamic) and equilibrium (static) were proposed to explain the common carp genome evolution between genome duplication and diploidization.

  9. An assessment of the spatial scale of local adaptation in brown trout (Salmo trutta L.): footprints of selection at microsatellite DNA loci

    DEFF Research Database (Denmark)

    Meier, Kristian; Hansen, Michael Møller; Bekkevold, Dorte;

    2011-01-01

    to spawning intrusion by farmed conspecifics that experience selection regimes fundamentally different from wild populations. This prompts the question if adaptive differences between wild populations and hatchery strains are more pronounced than between different wild populations? We addressed these issues...... of outliers between regions was evident. There was no evidence for more outliers in comparisons involving hatchery trout, but the loci under putative selection generally were not the same as those found to be outliers between wild populations. Our study supports the notion of local adaption being increasingly......Local adaptation is considered a paradigm in studies of salmonid fish populations. Yet, little is known about the geographical scale of local adaptation. Is adaptive divergence primarily evident at the scale of regions or individual populations? Also, many salmonid populations are subject...

  10. MICROSATELLITE ALTERATION AND ITS CHARACTERISTICS IN COLORECTAL CARCINOMA

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Objective: To determine the role of microsatellite alterations incarcinogenesis of colorectal carcinoma (CRC). Methods: Alterations of 10 microsatellite loci from 5 different chromosomes were detected in 92 colorectal cancers and their paired normal mucosa by PCR, denatured polyacrylamide gel electrophoresis and silver staining. Associations of microsatellite alterations with clinopathologic parameters were statistically clarified.Results: Alterations of microsatellite were classified into microsatellite instability type I, type II and loss of heterozygosity (LOH). The carcinoma with ≥30% loci microsatellite alterations was defined as replication error(RER) positive tumors. Of 92 cases, 14 were RER+. Microsatellite alterations of P53(1) and D18S363 loci (64.29% ) was most commonly identified in the RER+ tumors. RER+ were more commonly seen in poorly differentiated carcinomas and tended to occur in mucoid carcinomas. The type of microsatellite alterations varied in different histological types of CRC. Conclusions: Microsatellite alteration is a common molecular event in CRC. Different microsatellite loci showed various biologic significance. P53(1) and D18S363 should be essentially detected loci that can show the RER status of tumors.

  11. Microsatellite instability confounds engraftment analysis of hematopoietic stem-cell transplantation.

    Science.gov (United States)

    Tseng, Li-Hui; Tang, Jih-Luh; Haley, Lisa; Beierl, Katie; Gocke, Christopher D; Eshleman, James R; Lin, Ming-Tseh

    2014-07-01

    Polymorphic short tandem-repeat, or microsatellite, loci have been widely used to analyze chimerism status after allogeneic hematopoietic stem-cell transplantation. In molecular diagnostic laboratories, it is recommended to calculate mixed chimerism for at least 2 informative loci and to avoid microsatellite loci on chromosomes with copy number changes. In this report, we show that microsatellite instability observed in 2 patients with acute leukemia may confound chimerism analysis. Interpretation errors may occur even if 2 to 3 loci are analyzed because of length variation in multiple microsatellite loci. Although microsatellite loci with length variation should not be selected for chimerism analysis, the presence of microsatellite instability, like copy number alteration because of aberrant chromosomes, provides evidence of recurrent or residual cancer cells after hematopoietic stem-cell transplantation.

  12. Sequence determinants of human microsatellite variability

    Directory of Open Access Journals (Sweden)

    Jakobsson Mattias

    2009-12-01

    Full Text Available Abstract Background Microsatellite loci are frequently used in genomic studies of DNA sequence repeats and in population studies of genetic variability. To investigate the effect of sequence properties of microsatellites on their level of variability we have analyzed genotypes at 627 microsatellite loci in 1,048 worldwide individuals from the HGDP-CEPH cell line panel together with the DNA sequences of these microsatellites in the human RefSeq database. Results Calibrating PCR fragment lengths in individual genotypes by using the RefSeq sequence enabled us to infer repeat number in the HGDP-CEPH dataset and to calculate the mean number of repeats (as opposed to the mean PCR fragment length, under the assumption that differences in PCR fragment length reflect differences in the numbers of repeats in the embedded repeat sequences. We find the mean and maximum numbers of repeats across individuals to be positively correlated with heterozygosity. The size and composition of the repeat unit of a microsatellite are also important factors in predicting heterozygosity, with tetra-nucleotide repeat units high in G/C content leading to higher heterozygosity. Finally, we find that microsatellites containing more separate sets of repeated motifs generally have higher heterozygosity. Conclusions These results suggest that sequence properties of microsatellites have a significant impact in determining the features of human microsatellite variability.

  13. Molecular Characterization of Colombian Yam Germoplasm by "Selective Amplificaron of M i c rósate l lite Polymorphic Loci" (SAMPL Caracterización molecular del germoplasma de ñame colombiano utilizando "Selective Amplificaron of Microsatellite Polymorphic Loci" (SAMPL en condiciones radioactivas

    Directory of Open Access Journals (Sweden)

    Buitrago Hurtado Gustavo

    2006-12-01

    Full Text Available En Colombia el æame (Dioscorea spp. ha sido un cultivo básico tradicional a pequeña y mediana escala de cultivadores de la Costa Atlántica para abastecer el consumo propio y el mercado local, convirtiéndose en una gran fuente de empleo durante muchos años, sin embargo el ñame es uno de los cultivos más susceptibles a enfermedades (vg. la antracnosis y virus. En la actualidad el cultivo ha ido recuperándose progresivamente de una drástica reducción en área, como en producción, permitiendo aparentes resultados benéficos para los productores. Es imprescindible para el futuro del cultivo, que los productores cuenten con variedades seleccio­nadas para incrementar la sostenibilidad y rentabilidad del cultivo. Sin embargo esas variedades no están disponibles en la naturaleza, sino que tienen que ser mejoradas. El mejoramiento del ñame es difícil y presupone un conocimiento de la diversidad genetica del germoplasma de Dioscorea en Colombia, la cual no se conoce todavía. Por estas razones nosotros caracterizamos las variedades de ñame colombiano utilizadas en campo, así como las silvestres con una técnica de biología molecular: Selective Amplification Microsatellite Polimorphic Loci (SAMPL. Se detectaron 160 bandas identificables, (de las cuales 56 fueron monomórficas, 35% del total, con un rango de 2.8 bandas polimórficas por análisis. Con la información anterior se construyó una matriz binaria que fue transformada en un dendograma utilizando el algoritmo UPGMA. La diversidad de la colección determinada con esta técnica fue de 0.0471 con una media de similaridad de 0.9529. Palabras clave: Dioscorea spp, microsatélites, DNAIn Colombia, yam (Dioscoreu spp. has been a basic and traditional crop for small-and medium-scale farmers. It has been an important source of family employment in the Colombian Atlantic Coast for the past several centuries. However, yam is the most fragüe crop regarding market issues and disease

  14. Isolation of microsatellite loci and population genetic structure analysis of wild Corbicula fluminea in Hongze Lake%河蚬微卫星引物筛选及洪泽湖野生群体遗传结构分析

    Institute of Scientific and Technical Information of China (English)

    丁怀宇; 姜虎成; 冯建彬; 孙骥; 李家乐

    2011-01-01

    利用磁珠富集法筛选了河蚬10对中高度多态性的微卫星引物,并分析了洪泽湖河蚬4个野生群体的遗传结构.结果表明,每个群体至少有4个位点经Bonferroni校正后显示杂合不足,显著偏离了Hardy -Weinberg平衡(P<0.013);4个群体平均期望杂合度均大于0.752,显示出较高的遗传多样性水平,蒋坝、临淮群体遗传多样性高于高良涧和老子山群体;突变-漂移平衡分析结果显示,4个群体在IAM模型下偏离了突变-漂移平衡,高良涧群体在TPM模型下偏离了突变-漂移平衡,且表现杂合过剩,说明少数群体即将或曾经经历瓶颈效应,群体数量已出现波动;群体间AMOVA分析表明,洪泽湖河蚬群体间遗传分化程度较低(FST=0.017 7<0.05),仅有1.77%的变异来自群体间,并没有形成显著的遗传结构,在种质资源保护和管理上可视作一个单元,这为河蚬种质资源保护和合理开发利用提供了理论指导.%Asian clam( Corbicula fluminea) is a commercially important freshwater bivalve in South and East Asia. However,food clam mainly comes from the wild resources,and the natural populations have declined greatly and rapidly due to overfishing and natural habitats degradation. In China, the germplasm resource protection zone of C. Fluminea has been set up in Hongze Lake to protect the natural resources. In this paper, genetic structure of four wild C. Fluminea populations in Hongze Lake was analysized using ten polymorphic microsatellite DNA loci isolated and characterized by magnetic beads enrichment methods. The results showed that at least four of the loci were observed to have significant heterozygosity deficiency and obvious deviations from Hardy-Weinberg equilibrium(P<0.013) after Bonferroni correction in the four populations. Although values of expected heterozygosity were all above 0.752 and displayed high genetic diversity in the four populations,the level of genetic diversity fluctuated

  15. Inheritance of 15 microsatellites in the Pacific oyster Crassostrea gigas: segregation and null allele identification for linkage analysis

    Institute of Scientific and Technical Information of China (English)

    LI Li; GUO Ximing; ZHANG Guofan

    2009-01-01

    Microsatellites were screened in a backcross family of the Pacific oyster, Crassostrea gigas. Fifteen microsatellite loci were distinguishable and polymorphic with 6 types of allele-combinations. Null alleles were detected in 46.7% of loci, accounting for 11.7% of the total alleles. Four loci did not segregate in Mendelian Ratios. Three linkage groups were identified among 7 of the 15 segregating loci. Fluorescence-based automated capillary electrophoresis (ABI 310 Genetic Analyzer) that used to detect the microsatellite loci, has been proved a fast, precise, and reliable method in microsatellite genotyping.

  16. Isolation and characterization of new set of microsatellite loci in Cryptocarya chinensis%厚壳桂新微卫星体分子标记的开发与应用

    Institute of Scientific and Technical Information of China (English)

    高丹丹; 王峥峰; 朱鹏; 叶万辉

    2011-01-01

    Habitat fragmentation is the main threat to global biodiversity. Common species could also greatly suffer from habitat fragmentation. As a result of the destruction of the monsoon evergreen broad-leaved forest in South China,Cryptocarya chinensis ,one of the climax species,is now patchily distributed. Because a few microsateilite loci reported previously might cause low resolution to detect asexual reproduction in this species,we reported a new set of microsatellite which will assist to detect the extensiveness of sexual and asexual reproduction at fine spatial scale in the future. Eleven microsatellite markers from repetitive NA enriched libraries for C. chinensis were developed.Twenty-one individuals from Dinghu Mountain in South China were used to characterize their polymorphism. The number of alleles of 11 loci ranged from two to three,observed end expected heterozygosities ranged from 0. 048 to 1. 000,and 0. 048 to 0. 535,respectively. Deviations from Hardy-Weinberg equilibrium were detected in 8 loci due to heterozygote excess (highly significant negative Fis). All locus pairs showed significant linkage disequilibrium at the 0. 05 significant level, but such significance disappeared alter Bonferroni correction. 20 of 21 detected individuals showed identical multilocus genotype. All these results conformed to the genetic characteristic of clonal species,confirming extensive clonal growth in C. chinensis.%生境破碎化是导致全球生物多样性危机的主要原因,即使常见物种也会受到很大影响.厚壳桂(Cryptocarya chinensis)是我国南亚热带季风常绿阔叶林群落演替顶极物种,由于这一森林植被的破坏而呈片断化分布.在以往的研究中,我们利用筛选到的一些微卫星体对其遗传多样性研究后发现其可能以无性生殖为主.为进一步证实这一发现,该文又报道了11个新微卫星体,这些新微卫星体和以往报道的微卫星体将有助于更好分辨厚壳桂的有性和无

  17. Microsatellite primers for fungus-growing ants

    DEFF Research Database (Denmark)

    Villesen, Palle; Gertsch, P J; Boomsma, JJ

    2002-01-01

    developed primers and earlier published primers that were developed for fungus-growing ants. A total of 20 variable microsatellite loci, developed for six different species of fungus-growing ants, are now available for studying the population genetics and colony kin-structure of these ants.......We isolated five polymorphic microsatellite loci from a library of two thousand recombinant clones of two fungus-growing ant species, Cyphomyrmex longiscapus and Trachymyrmex cf. zeteki. Amplification and heterozygosity were tested in five species of higher attine ants using both the newly...

  18. Microsatellite Primers for Fungus-Growing Ants

    DEFF Research Database (Denmark)

    Villesen Fredsted, Palle; Gertsch, Pia J.; Boomsma, Jacobus Jan (Koos)

    2002-01-01

    developed primers and earlier published primers that were developed for fungus-growing ants. A total of 20 variable microsatellite loci, developed for six different species of fungus-growing ants, are now available for studying the population genetics and colony kin-structure of these ants.......We isolated five polymorphic microsatellite loci from a library of two thousand recombinant clones of two fungus-growing ant species, Cyphomyrmex longiscapus and Trachymyrmex cf. zeteki. Amplification and heterozygosity were tested in five species of higher attine ants using both the newly...

  19. Microsatellite Primers for Fungus-Growing Ants

    DEFF Research Database (Denmark)

    Villesen Fredsted, Palle; Gertsch, Pia J.; Boomsma, Jacobus Jan (Koos)

    2002-01-01

    We isolated five polymorphic microsatellite loci from a library of two thousand recombinant clones of two fungus-growing ant species, Cyphomyrmex longiscapus and Trachymyrmex cf. zeteki. Amplification and heterozygosity were tested in five species of higher attine ants using both the newly...... developed primers and earlier published primers that were developed for fungus-growing ants. A total of 20 variable microsatellite loci, developed for six different species of fungus-growing ants, are now available for studying the population genetics and colony kin-structure of these ants....

  20. Microsatellite primers for fungus-growing ants

    DEFF Research Database (Denmark)

    Villesen, Palle; Gertsch, P J; Boomsma, JJ

    2002-01-01

    We isolated five polymorphic microsatellite loci from a library of two thousand recombinant clones of two fungus-growing ant species, Cyphomyrmex longiscapus and Trachymyrmex cf. zeteki. Amplification and heterozygosity were tested in five species of higher attine ants using both the newly...... developed primers and earlier published primers that were developed for fungus-growing ants. A total of 20 variable microsatellite loci, developed for six different species of fungus-growing ants, are now available for studying the population genetics and colony kin-structure of these ants....

  1. Microsatellites as targets of natural selection.

    Science.gov (United States)

    Haasl, Ryan J; Payseur, Bret A

    2013-02-01

    The ability to survey polymorphism on a genomic scale has enabled genome-wide scans for the targets of natural selection. Theory that connects patterns of genetic variation to evidence of natural selection most often assumes a diallelic locus and no recurrent mutation. Although these assumptions are suitable to selection that targets single nucleotide variants, fundamentally different types of mutation generate abundant polymorphism in genomes. Moreover, recent empirical results suggest that mutationally complex, multiallelic loci including microsatellites and copy number variants are sometimes targeted by natural selection. Given their abundance, the lack of inference methods tailored to the mutational peculiarities of these types of loci represents a notable gap in our ability to interrogate genomes for signatures of natural selection. Previous theoretical investigations of mutation-selection balance at multiallelic loci include assumptions that limit their application to inference from empirical data. Focusing on microsatellites, we assess the dynamics and population-level consequences of selection targeting mutationally complex variants. We develop general models of a multiallelic fitness surface, a realistic model of microsatellite mutation, and an efficient simulation algorithm. Using these tools, we explore mutation-selection-drift equilibrium at microsatellites and investigate the mutational history and selective regime of the microsatellite that causes Friedreich's ataxia. We characterize microsatellite selective events by their duration and cost, note similarities to sweeps from standing point variation, and conclude that it is premature to label microsatellites as ubiquitous agents of efficient adaptive change. Together, our models and simulation algorithm provide a powerful framework for statistical inference, which can be used to test the neutrality of microsatellites and other multiallelic variants.

  2. Dinucleotide repeat microsatellite markers for buck's-horn plantain (Plantago coronopus)

    NARCIS (Netherlands)

    Koorevaar, G.N.; Ivanovic, S.; Van Damme, J.M.M.; Koelewijn, H.P.; Van 't Westende, W.P.C.; Smulders, M.J.M.; Vosman, B.

    2002-01-01

    Eleven polymorphic microsatellite loci were obtained from a GA enriched genomic library, constructed from DNA of buck's-horn plantain (Plantago coronopus). The microsatellite loci were tested on 24 genotypes. These plants were collected from meadows along the coast, located on 11 sites ranging from

  3. Characterization of nine polymorphic microsatellite markers in sprat ( Sprattus sprattus L.)

    DEFF Research Database (Denmark)

    Dailianis, T.; Limborg, Morten; Hanel, R.;

    2008-01-01

    Nine polymorphic microsatellites were isolated from sprat (Sprattus sprattus) using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC)(12) probe. The loci showed different variation patterns in a Baltic Sea population (44 individuals) with mean number...... of alleles at 12.7 and mean observed heterozygosity at 0.78. These microsatellite loci are expected to be used for taxonomic considerations in sprat, stock differentiation and population genetic analysis....

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

    OpenAIRE

    Jakaria; M.S.A. Zein; S. Sulandari; Subandriyo,; Muladno

    2014-01-01

    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 ...

  5. Microsatellite Markers for Raspberries and Blackberries

    Science.gov (United States)

    Twelve microsatellites were isolated from SSR-enriched genomic libraries of Rubus idaeus L.‘Meeker’ red raspberry (diploid) and R. loganobaccus L. H. Bailey ‘Marion’ blackberry-raspberry hybrid (hexaploid). These primer pairs, with the addition of one developed from a GenBank R. idaeus sequence, w...

  6. Validation of EST-derived microsatellite markers for two Cerrado-endemic Campomanesia (Myrtaceae) species.

    Science.gov (United States)

    Miranda, E A G C; Boaventura-Novaes, C R D; Braga, R S; Reis, E F; Pinto, J F N; Telles, M P C

    2016-03-04

    We assessed the transferability of 120 EST-derived Eucalyptus microsatellite primers to Campomanesia adamantium and C. pubescens. Both species are berry trees native to the Brazilian Cerrado, and population genetic information is poor. Twelve markers were used to analyze the genetic variability of four sampled populations. Regarding DNA extraction, we sampled leaf tissues from two populations of each species (80 individuals). Of the 120 primers evaluated, 87 did not amplify any PCR products, and 21 rendered nonspecific amplification. Twelve primers were successfully transferred, providing a low combined probability of genetic identity for both species (5.718 x 10(-10) for C. adamantium; 1.182 x 10(-11) for C. pubescens) and a high probability of paternity exclusion (0.99939 for C. adamantium; 0.99982 for C. pubescens). The average number of alleles in the polymorphic loci was 6.8 for C. adamantium and 7.8 for C. pubescens, ranging from 2 to 16 alleles per locus. The observed heterozygosity values for C. adamantium and C. pubescens were 0.504 and 0.503, respectively, and the expected heterozygosity values for C. adamantium and C. pubescens were 0.517 and 0.579, respectively. The populations exhibited structured genetic variability with qP values of 0.105 for C. adamantium and 0.249 for C. pubescens. Thus, we concluded that these 12 microsatellite markers, transferred from Eucalyptus, were efficient for population genetic studies of C. adamantium and C. pubescens.

  7. Evaluation of microsatellite markers for populations studies and forensic identification of African lions (Panthera leo).

    Science.gov (United States)

    Miller, Susan M; Harper, Cindy K; Bloomer, Paulette; Hofmeyr, Jennifer; Funston, Paul J

    2014-01-01

    The South African lion (Panthera leo) population is highly fragmented. One-third of its wild lions occur in small (<1000 km(2)) reserves. These lions were reintroduced from other areas of the species' historical range. Management practices on these reserves have not prioritized genetic provenance or heterozygosity. These trends potentially constrain the conservation value of these lions. To ensure the best management and long-term survival of these subpopulations as a viable collective population, the provenance and current genetic diversity must be described. Concurrently, poaching of lions to supply a growing market for lion bones in Asia may become a serious conservation challenge in the future. Having a standardized, validated method for matching confiscated lion parts with carcasses will be a key tool in investigating these crimes. We evaluated 28 microsatellites in the African lion using samples from 18 small reserves and 1 captive facility in South Africa, two conservancies in Zimbabwe, and Kruger National and Kgalagadi Transfrontier Parks to determine the loci most suited for population management and forensic genetic applications. Twelve microsatellite loci with a match probability of 1.1×10(-5) between siblings were identified for forensics. A further 10 could be added for population genetics studies.

  8. Microsatellite markers for northern red oak (Fagaceae: Quercus rubra)

    Science.gov (United States)

    Preston R. Aldrich; Charles H. Michler; Weilin Sun; Jeanne Romero-Severson

    2002-01-01

    We provide primer sequences for 14 (GA)n microsatellite loci developed from northern red oak, an important timber species. We screened loci using two sets of samples. A parent-offspring set included DNA from seven acorns collected from one mother tree along with maternal DNA, to determine that all progeny carried a maternal allele at each locus....

  9. megasat: automated inference of microsatellite genotypes from sequence data.

    Science.gov (United States)

    Zhan, Luyao; Paterson, Ian G; Fraser, Bonnie A; Watson, Beth; Bradbury, Ian R; Nadukkalam Ravindran, Praveen; Reznick, David; Beiko, Robert G; Bentzen, Paul

    2017-03-01

    megasat is software that enables genotyping of microsatellite loci using next-generation sequencing data. Microsatellites are amplified in large multiplexes, and then sequenced in pooled amplicons. megasat reads sequence files and automatically scores microsatellite genotypes. It uses fuzzy matches to allow for sequencing errors and applies decision rules to account for amplification artefacts, including nontarget amplification products, replication slippage during PCR (amplification stutter) and differential amplification of alleles. An important feature of megasat is the generation of histograms of the length-frequency distributions of amplification products for each locus and each individual. These histograms, analogous to electropherograms traditionally used to score microsatellite genotypes, enable rapid evaluation and editing of automatically scored genotypes. megasat is written in Perl, runs on Windows, Mac OS X and Linux systems, and includes a simple graphical user interface. We demonstrate megasat using data from guppy, Poecilia reticulata. We genotype 1024 guppies at 43 microsatellites per run on an Illumina MiSeq sequencer. We evaluated the accuracy of automatically called genotypes using two methods, based on pedigree and repeat genotyping data, and obtained estimates of mean genotyping error rates of 0.021 and 0.012. In both estimates, three loci accounted for a disproportionate fraction of genotyping errors; conversely, 26 loci were scored with 0-1 detected error (error rate ≤0.007). Our results show that with appropriate selection of loci, automated genotyping of microsatellite loci can be achieved with very high throughput, low genotyping error and very low genotyping costs.

  10. Microsatellite DNA capture from enriched libraries.

    Science.gov (United States)

    Gonzalez, Elena G; Zardoya, Rafael

    2013-01-01

    Microsatellites are DNA sequences of tandem repeats of one to six nucleotides, which are highly polymorphic, and thus the molecular markers of choice in many kinship, population genetic, and conservation studies. There have been significant technical improvements since the early methods for microsatellite isolation were developed, and today the most common procedures take advantage of the hybrid capture methods of enriched-targeted microsatellite DNA. Furthermore, recent advents in sequencing technologies (i.e., next-generation sequencing, NGS) have fostered the mining of microsatellite markers in non-model organisms, affording a cost-effective way of obtaining a large amount of sequence data potentially useful for loci characterization. The rapid improvements of NGS platforms together with the increase in available microsatellite information open new avenues to the understanding of the evolutionary forces that shape genetic structuring in wild populations. Here, we provide detailed methodological procedures for microsatellite isolation based on the screening of GT microsatellite-enriched libraries, either by cloning and Sanger sequencing of positive clones or by direct NGS. Guides for designing new species-specific primers and basic genotyping are also given.

  11. Detected microsatellite polymorphisms in genetically altered inbred mouse strains.

    Science.gov (United States)

    Du, Xiaoyan; Cui, Jing; Wang, Chao; Huo, Xueyun; Lu, Jing; Li, Yichen; Chen, Zhenwen

    2013-08-01

    Microsatellites are 50-200 repetitive DNA sequences composed of 1- to 6-base-pair-long reiterative motifs within the genome. They are vulnerable to DNA modifications, such as recombination and/or integration, and are recognized as "sentinel" DNA. Our previous report indicated that the genotypes of the microsatellite loci could change from mono- to poly-morphisms (CMP) in gene knockout (KO) mice, implying that genetic modification induces microsatellite mutation. However, it is still unclear whether the random insertion of DNA fragments into mice genomes produced via transgene (Tg) or N-ethyl-N-nitrosourea (ENU) would also result in microsatellite mutations or microsatellite loci genotypes changes. This study was designed to find possible clues to answer this question. In brief, 198 microsatellite loci that were distributed among almost all of the chromosomes (except for the Y) were examined through polymerase chain reaction to screen possible CMPs in six Tg strains. First, for each strain, the microsatellite sequences of all loci were compared between Tg and the corresponding background strain to exclude genetic interference. Simultaneously, to exclude spontaneous mutation-related CMPs that might exist in the examined six strains, mice from five spontaneously mutated inbred strains were used as the negative controls. Additionally, the sequences of all loci in these spontaneous mutated mice were compared to corresponding genetic background controls. The results showed that 40 of the 198 (20.2%) loci were identified as having CMPs in the examined Tg mice strains. The CMP genotypes were either homozygous or heterozygous compared to the background controls. Next, we applied the 40 CMP positive loci in ENU-mutated mice and their corresponding background controls. After that, a general comparison of CMPs that exist among Tg, ENU-treated and KO mouse strains was performed. The results indicated that four (D11mit258, D13mit3, D14mit102 and DXmit172) of the 40 (10%) CMP

  12. Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline.

    Science.gov (United States)

    Fernandez-Silva, Iria; Whitney, Jonathan; Wainwright, Benjamin; Andrews, Kimberly R; Ylitalo-Ward, Heather; Bowen, Brian W; Toonen, Robert J; Goetze, Erica; Karl, Stephen A

    2013-01-01

    Microsatellites are the markers of choice for a variety of population genetic studies. The recent advent of next-generation pyrosequencing has drastically accelerated microsatellite locus discovery by providing a greater amount of DNA sequencing reads at lower costs compared to other techniques. However, laboratory testing of PCR primers targeting potential microsatellite markers remains time consuming and costly. Here we show how to reduce this workload by screening microsatellite loci via bioinformatic analyses prior to primer design. Our method emphasizes the importance of sequence quality, and we avoid loci associated with repetitive elements by screening with repetitive sequence databases available for a growing number of taxa. Testing with the Yellowstripe Goatfish Mulloidichthys flavolineatus and the marine planktonic copepod Pleuromamma xiphias we show higher success rate of primers selected by our pipeline in comparison to previous in silico microsatellite detection methodologies. Following the same pipeline, we discover and select microsatellite loci in nine additional species including fishes, sea stars, copepods and octopuses.

  13. DNA microsatellite analysis for tomato genetic differentiation

    Directory of Open Access Journals (Sweden)

    Miskoska-Milevska Elizabeta

    2015-01-01

    Full Text Available Commonly used method for determination of the genetic diversity among the populations is the test for genetic differentiation. DNA microsatellite markers are usually used to investigate the genetic structure of natural populations. The aim of this study was to evaluate the applicability of eight DNA microsatellite loci (LECH13, LE21085, LEMDDNa, LEEF1Aa, LELEUZIP, LE20592, TMS9 and LE2A11 in genetic differentiation of six morphologically different tomato varieties (var. grandifolium from subsp. cultum; var. cerasiforme - red and yellow, var. pruniforme and var. pyriforme from subsp. subspontaneum; and var. racemigerum from subsp. spontaneum. The fragment analyses was performed using Applied Biosystems DNA analyzer (ABI 3130 and GeneMapper® Software program. The data were analysed using the specific program Power Marker Software. The average number of detected alleles was 3,625. Also, the average PIC value for all 8 DNA microsatellites loci was 0,3571. The genetic differentiation test in the researched tomato subspecies showed minor differentiation for locus LELEUZIP (- 0,0009, modest differentiation for locus LECH13 (0,0896, locus LEMDDNa (0,0896 and locus LE21085 (0,0551 and major differentiation for locus LE2A11 (0,7633, locus LEEF1Aa (0,6167, locus TMS9 (0.4967 and locus LE20592 (0,4263. On the other hand, in the estimated tomato varieties, locus LE21085 (0,0297, locus LECH13 (0,0256 and locus LELEUZIP (0,0005 showed minor differentiation, locus LEMDDNa (0,1333 showed modest differentiation, while locus TMS9 (0,5929, locus LEEF1Aa (0,5006, locus LE2A11 (0,4013 and locus LE20592 (0,2606 showed major differentiation. The eight DNA microsatellite loci can be applicable solution for tomato genetic differentiation. The overall results suggest that these microsatellite loci could be used in further population genetic studies of tomatoes.

  14. Characterization of polymorphic microsatellite DNA markers in the black-tailed godwit (Limosa limosa : Aves)

    NARCIS (Netherlands)

    Verkuil, Yvonne I.; Trimbos, Krijn; Haddrath, Oliver; Baker, Allan J.; Piersma, Theunis

    2009-01-01

    We isolated and tested 16 microsatellite loci in black-tailed godwits from the Netherlands (Limosa limosa limosa), and from Australasia (subspecies melanuroides). One locus was monomorphic, two loci had null-alleles and one was significantly heterozygote deficient. The remaining 12 polymorphic loci

  15. Microsatellite markers characterized in the barn owl (Tyto alba) and of high utility in other owls (Strigiformes: AVES).

    Science.gov (United States)

    Klein, Akos; Horsburgh, Gavin J; Küpper, Clemens; Major, Agnes; Lee, Patricia L M; Hoffmann, Gyula; Mátics, Róbert; Dawson, Deborah A

    2009-11-01

    We have identified 15 polymorphic microsatellite loci for the barn owl (Tyto alba), five from testing published owl loci and 10 from testing non-owl loci, including loci known to be of high utility in passerines and shorebirds. All 15 loci were sequenced in barn owl, and new primer sets were designed for eight loci. The 15 polymorphic loci displayed two to 26 alleles in 56-58 barn owls. When tested in 10 other owl species (n = 1-6 individuals), between four and nine loci were polymorphic per species. These loci are suitable for studies of population structure and parentage in owls.

  16. Directed isolation and mapping of microsatellites from swine Chromosome 1q telomeric region through microdissection and RH mapping.

    Science.gov (United States)

    Sarker, N; Hawken, R J; Takahashi, S; Alexander, L J; Awata, T; Schook, L B; Yasue, H

    2001-07-01

    Several quantitative trait loci (QTLs) (vertebrate number, birth weight, age at puberty, growth rate, gestation length, and backfat depth) have been independently mapped to the distal region of swine Chromosome (SSC) 1q in several resource populations. In order to improve the map resolution and refine these QTLs more precisely on SSC1q, we have isolated and mapped additional microsatellites (ms), using chromosome microdissection and radiation hybrid (RH) mapping. Five copies of the telomeric region of SSC1q were microdissected from metaphase spreads and pooled. The chromosomal fragment DNA was randomly amplified by using degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR), enriched for ms, and subcloned into a PCR vector. Screening of subsequent clones with ms probes identified 23 unique ms sequences. Fifteen of these (65%) were subjected to radiation hybrid (RH) mapping by using the INRA-University of Minnesota porcine RH panel (IMpRH); and the remaining eight were not suited for the RH mapping. Twelve microsatellites were assigned to SSC1q telomeric region of IMpRH map (LOD >6), and three remain unlinked (LOD pig. In summary, we have used microdissection and radiation hybrid mapping to clone and map 12 new microsatellites to the swine gene map to increase the resolution of SSC1q in the region of known QTLs.

  17. Microsatellite Primers for the Pacific Northwest Conifer Callitropsis nootkatensis (Cupressaceae

    Directory of Open Access Journals (Sweden)

    Tara N. Jennings

    2013-09-01

    Full Text Available Premise of the study: Microsatellite primers were developed for Nootka cypress (Callitropsis nootkatensis to provide quantitative measures for gene conservation that can assist in guiding management decisions for a species experiencing climate-induced decline. Methods and Results: Using multiplexed massively parallel sequencing, we identified 136,785 microsatellite-containing sequences from 489,625 Illumina paired-end 80-bp reads. After stringent filtering, we selected 144 primer pairs and screened variation at these loci in five populations of C. nootkatensis. Loci show between three and 36 dinucleotide repeats per locus, with an average of 13. Screening of these markers in the Pacific Northwest relative Chamaecyparis lawsoniana demonstrated no marker transferability. This finding highlights the narrow taxonomic utility of microsatellite markers in Callitropsis. Conclusions: These microsatellites show high polymorphism and can be used for routine screening of natural variation in Callitropsis nootkatensis, and will be particularly helpful in identifying clones and inbred relatives at the stand-level.

  18. Designing of an artificial neural network model to evaluate the association of three combined Y-specific microsatellite loci on the actual and predicted postthaw motility in crossbred bull semen.

    Science.gov (United States)

    Deb, Rajib; Singh, Umesh; Raja, Thirvvothur Venkatesan; Kumar, Sushil; Tyagi, Shrikant; Alyethodi, Rafeeque R; Alex, Rani; Sengar, Gyanendra; Sharma, Sheetal

    2015-06-01

    The freezing of bull semen significantly hamper the motility of sperm which reduces the conception rate in dairy cattle. The prediction of postthaw motility (PTM) before freezing will be useful to take the decision on discarding or freezing of the germplasm. The artificial neural network (ANN) methodology found to be useful in prediction and classification problems related to animal science, and hence, the present study was undertaken to compare the efficiency of ANN in prediction of PTM on the basis of the number of ejaculates, volume, and concentration of sperms. The combined effect of Y-specific microsatellite alleles on the actual and predicted PTM was also studied. The results revealed that the prediction accuracy of PTM based on the semen quality parameters was comparatively lower because of higher variability in the data set. The ANN gave better prediction accuracy (34.88%) than the multiple regression analysis models (32.04%). The root mean square error was lower for ANN (8.4353) than that in the multiple regression analysis (8.6168). The haplotype or combined effect of microsatellite alleles on actual and predicted PTM was found to be highly significant (P < 0.01). On the basis of results, it was concluded that the ANN methodology can be used for prediction of PTM in crossbred bulls.

  19. Highly polymorphic microsatellite markers for Radix balthica (Linnaeus 1758).

    Science.gov (United States)

    Salinger, M; Pfenninger, M

    2009-07-01

    We present data for eight polymorphic microsatellite markers isolated from a microsatellite-enriched DNA library for the freshwater snail Radix balthica. Three of them were specific for R. balthica while five also amplified polymorphic products in two congeneric species. Test application on populations from all over the species range has shown that these loci are highly informative for analysing population structure and estimating migration rates. Observed deviations from Hardy-Weinberg equilibrium are attributed to a mixed mating system.

  20. A Phylogenetic Index for Cichlid Microsatellite Primers

    Directory of Open Access Journals (Sweden)

    Robert D. Kunkle

    2010-01-01

    Full Text Available Microsatellites abound in most organisms and have proven useful for a range of genetic and genomic studies. Once primers have been created, they can be applied to populations or taxa that have diverged from the source taxon. We use PCR amplification, in a 96-well format, to determine the presence and absence of 46 microsatellite loci in 13 cichlid species. At least one primer set amplified a product in each species tested, and some products were present in nearly all species. These results are compared to the known phylogenetic relationships among cichlids. While we do not address intraspecies variation, our results present a phylogenetic index for the success of microsatellite PCR primer product amplification, thus providing information regarding a collection of primers that are applicable to wide range of species. Through the use of such a uniform primer panel, the potential impact for cross species would be increased.

  1. Analysis of microsatellite polymorphism in inbred knockout mice.

    Science.gov (United States)

    Zuo, Baofen; Du, Xiaoyan; Zhao, Jing; Yang, Huixin; Wang, Chao; Wu, Yanhua; Lu, Jing; Wang, Ying; Chen, Zhenwen

    2012-01-01

    Previously, we found that the genotype of 42 out of 198 mouse microsatellite loci, which are distributed among all chromosomes except the Y chromosome, changed from monomorphism to polymorphism (CMP) in a genetically modified inbred mouse strain. In this study, we further examined whether CMP also relates to the homologous recombination in gene knockout (KO) mouse strains. The same 42 microsatellite loci were analyzed by polymerase chain reaction (PCR) in 29 KO inbred mouse strains via short tandem sequence repeat (STR) scanning and direct sequence cloning to justify microsatellite polymorphisms. The C57BL/6J and 129 mouse strains, from which these 29 KO mice were derived, were chosen as the background controls. The results indicated that 10 out of 42 (23.8%) loci showed CMP in some of these mouse strains. Except for the trinucleotide repeat locus of D3Mit22, which had microsatellite CMP in strain number 9, the core sequences of the remaining 41 loci were dinucleotide repeats, and 9 out of 41 (21.95%) showed CMPs among detected mouse strains. However, 11 out of 29 (37.9%) KO mice strains were recognized as having CMPs. The popular dinucleotide motifs in CMP were (TG)(n) (50%, 2/4), followed by (GT)(n) (27.27%, 3/11) and (CA)(n) (23.08%, 3/13). The microsatellite CMP in (CT)(n) and (AG)(n) repeats were 20% (1/5). According to cloning sequencing results, 6 KO mouse strains showed insertions of nucleotides whereas 1 showed a deletion. Furthermore, 2 loci (D13Mit3 and D14Mit102) revealed CMP in 2 strains, and mouse strain number 9 showed CMPs in two loci (D3Mit22 and D13Mit3) simultaneously. Collectively, these results indicated that microsatellite polymorphisms were present in the examined inbred KO mice.

  2. Analysis of microsatellite polymorphism in inbred knockout mice.

    Directory of Open Access Journals (Sweden)

    Baofen Zuo

    Full Text Available Previously, we found that the genotype of 42 out of 198 mouse microsatellite loci, which are distributed among all chromosomes except the Y chromosome, changed from monomorphism to polymorphism (CMP in a genetically modified inbred mouse strain. In this study, we further examined whether CMP also relates to the homologous recombination in gene knockout (KO mouse strains. The same 42 microsatellite loci were analyzed by polymerase chain reaction (PCR in 29 KO inbred mouse strains via short tandem sequence repeat (STR scanning and direct sequence cloning to justify microsatellite polymorphisms. The C57BL/6J and 129 mouse strains, from which these 29 KO mice were derived, were chosen as the background controls. The results indicated that 10 out of 42 (23.8% loci showed CMP in some of these mouse strains. Except for the trinucleotide repeat locus of D3Mit22, which had microsatellite CMP in strain number 9, the core sequences of the remaining 41 loci were dinucleotide repeats, and 9 out of 41 (21.95% showed CMPs among detected mouse strains. However, 11 out of 29 (37.9% KO mice strains were recognized as having CMPs. The popular dinucleotide motifs in CMP were (TG(n (50%, 2/4, followed by (GT(n (27.27%, 3/11 and (CA(n (23.08%, 3/13. The microsatellite CMP in (CT(n and (AG(n repeats were 20% (1/5. According to cloning sequencing results, 6 KO mouse strains showed insertions of nucleotides whereas 1 showed a deletion. Furthermore, 2 loci (D13Mit3 and D14Mit102 revealed CMP in 2 strains, and mouse strain number 9 showed CMPs in two loci (D3Mit22 and D13Mit3 simultaneously. Collectively, these results indicated that microsatellite polymorphisms were present in the examined inbred KO mice.

  3. Microsatellite genotyping reveals a signature in breast cancer exomes.

    Science.gov (United States)

    McIver, L J; Fonville, N C; Karunasena, E; Garner, H R

    2014-06-01

    Genomic instability at microsatellite loci is a hallmark of many cancers, including breast cancer. However, much of the genomic variation and many of the hereditary components responsible for breast cancer remain undetected. We hypothesized that variation at microsatellites could provide additional genomic markers for breast cancer risk assessment. A total of 1,345 germline and tumor DNA samples from individuals diagnosed with breast cancer, exome sequenced as part of The Cancer Genome Atlas, were analyzed for microsatellite variation. The comparison group for our analysis, representing healthy individuals, consisted of 249 females which were exome sequenced as part of the 1,000 Genomes Project. We applied our microsatellite-based genotyping pipeline to identify 55 microsatellite loci that can distinguish between the germline of individuals diagnosed with breast cancer and healthy individuals with a sensitivity of 88.4 % and a specificity of 77.1 %. Further, we identified additional microsatellite loci that are potentially useful for distinguishing between breast cancer subtypes, revealing a possible fifth subtype. These findings are of clinical interest as possible risk diagnostics and reveal genes that may be of potential therapeutic value, including genes previously not associated with breast cancer.

  4. Tools for assessing kinship, population structure, phylogeography, and interspecific hybridization in Asian carps invasive to the Mississippi River, USA: isolation and characterization of novel tetranucleotide microsatellite DNA loci in silver carp Hypophthalmichthys molitrix

    Science.gov (United States)

    King, T.L.; Eackles, M.S.; Chapman, D.C.

    2011-01-01

    We document the isolation and characterization of novel tetranucleotide microsatellite DNA markers for the invasive silver carp Hypophthalmichthys molitrix and provide the results of cross-species amplification for three additional invasive carp species: bighead (H. nobilis), grass (Ctenopharyngodon idella) and black (Mylopharyngodon piceus). In the target species these markers yielded levels of allelic diversity (average 4.4 alleles/locus) and heterozygosity (average 54.7%) sufficient to: (1) provide unique multilocus genotypes; (2) delineate kinship relationships; (3) differentiate populations/species; (4) estimate effective population sizes; and (5) provide unique demographic perspectives for control or eradication. Currently these markers are being utilized to determine the degree of introgressive hybridization between H. molitrix and H. nobilis, to quantify gene flow between different sub-basins established in the central United States, and to assess the demographic status of sub-basin groups. This information will be critically important in the management/control of these invasive species.

  5. Microsatellite Markers in the Western Prairie Fringed Orchid, Platanthera praeclara (Orchidaceae

    Directory of Open Access Journals (Sweden)

    Andrew A. Ross

    2013-04-01

    Full Text Available Premise of the study: Primers for 31 microsatellite-containing loci were developed for the threatened orchid Platanthera praeclara to enable characterization of the population genetics of this tallgrass prairie native. Methods and Results: Sixteen polymorphic microsatellite loci were identified from four populations. Six of these loci were not in linkage disequilibrium. The average number of alleles per locus per population ranged from 6.4 to 8.9. Conclusions: The results indicate that six of the polymorphic loci will be useful in future studies of population structure, gene flow, and genetic diversity.

  6. Microsatellite marker isolation and development for the giant Pacific Octopus (Enteroctopus dofleini)

    Science.gov (United States)

    Toussaint, Rebecca K.; Sage, G. Kevin; Talbot, Sandra L.; Scheel, David

    2012-01-01

    We isolated and developed 18 novel microsatellite markers for the giant Pacific octopus (Enteroctopus dofleini) and examined them for 31 individuals from Prince William Sound (PWS), Alaska. These loci displayed moderate levels of allelic diversity (averaging 11 alleles per locus) and heterozygosity (averaging 65%). Seven loci deviated from Hardy–Weinberg Equilibrium (HWE) due to heterozygote deficiency for the PWS population, although deviations were not observed for all these loci in other populations, suggesting the PWS population is not in mutation-drift equilibrium. These novel microsatellite loci yielded sufficient genetic diversity for potential use in population genetics, individual identification, and parentage studies.

  7. Microsatellite DNA markers discriminate between two Octopus vulgaris (Cephalopoda: Octopoda) fisheries along the northwest African coast

    National Research Council Canada - National Science Library

    Murphy, J.M; Balguerias, E; Key, L.N; Boyle, P.R

    2002-01-01

    .... This study aims to determine, using microsatellite DNA loci, whether octopus in the two fisheries are genetically distinct and to try to locate the origin of the samples by comparison with samples...

  8. Application of a double-enrichment procedure for microsatellite isolation and the use of tailed primers for high throughput genotyping

    Directory of Open Access Journals (Sweden)

    Fábio Mendonça Diniz

    2007-03-01

    Full Text Available The number of microsatellite loci and their allelic diversity contribute to increase accuracy and informativity of genetic estimates, however, the isolation of microsatellite loci is not only laborious but also quite expensive. We used (GATAn and (GACAn tetranucleotide probes and single- and double-enrichment hybridization to construct and screen a genomic library with an increased proportion of DNA fragments containing repeat motifs. Repeats were found using both types of hybridization but the double-enrichment procedure recovered sequences of which 100% contained (GATAn and (GACAn motifs. Microsatellite loci primers were then designed with an M13R-tail or CAG-tag to produce scorable PCR products with minimal stutter. The approach used in this study suggests that double-enrichment is a worthwhile strategy when isolating repeat motifs from eukaryotic genomes. Moreover, the use of tailed microsatellite primers provides increased resolution for compound microsatellite loci, with a significant decrease in costs.

  9. Isolation and characterization of eight polymorphic microsatellites for the spotted spiny lobster, Panulirus guttatus

    Directory of Open Access Journals (Sweden)

    Nathan Truelove

    2016-01-01

    Full Text Available Microsatellite sequences were isolated from enriched genomic libraries of the spotted spiny lobster, Panulirus guttatus using 454 pyrosequencing. Twenty-nine previously developed polymerase chain reaction primer pairs of Panulirus argus microsatellite loci were also tested for cross-species amplification in Panulirus guttatus. In total, eight consistently amplifying, and polymorphic loci were characterized for 57 individuals collected in the Florida Keys and Bermuda. The number of alleles per locus ranged from 8 to 20 and observed heterozygosities ranged from 0.409 to 0.958. Significant deviations from Hardy–Weinberg equilibrium were found in one locus from Florida and three loci from Bermuda. Quality control testing indicated that all loci were easy to score, highly polymorphic and showed no evidence of linkage disequilibrium. Null alleles were detected in three loci with moderate frequencies ranging from (20% to 22%. These eight microsatellites provide novel molecular markers for future conservation genetics research of P. guttatus.

  10. Evidence for widespread convergent evolution around human microsatellites.

    Directory of Open Access Journals (Sweden)

    Edward J Vowles

    2004-08-01

    Full Text Available Microsatellites are a major component of the human genome, and their evolution has been much studied. However, the evolution of microsatellite flanking sequences has received less attention, with reports of both high and low mutation rates and of a tendency for microsatellites to cluster. From the human genome we generated a database of many thousands of (AC(n flanking sequences within which we searched for common characteristics. Sequences flanking microsatellites of similar length show remarkable levels of convergent evolution, indicating shared mutational biases. These biases extend 25-50 bases either side of the microsatellite and may therefore affect more than 30% of the entire genome. To explore the extent and absolute strength of these effects, we quantified the observed convergence. We also compared homologous human and chimpanzee loci to look for evidence of changes in mutation rate around microsatellites. Most models of DNA sequence evolution assume that mutations are independent and occur randomly. Allowances may be made for sites mutating at different rates and for general mutation biases such as the faster rate of transitions over transversions. Our analysis suggests that these models may be inadequate, in that proximity to even very short microsatellites may alter the rate and distribution of mutations that occur. The elevated local mutation rate combined with sequence convergence, both of which we find evidence for, also provide a possible resolution for the apparently contradictory inferences of mutation rates in microsatellite flanking sequences.

  11. Design and implementation of degenerate microsatellite primers for the mammalian clade.

    Directory of Open Access Journals (Sweden)

    Emmanuel Buschiazzo

    Full Text Available Microsatellites are popular genetic markers in molecular ecology, genetic mapping and forensics. Unfortunately, despite recent advances, the isolation of de novo polymorphic microsatellite loci often requires expensive and intensive groundwork. Primers developed for a focal species are commonly tested in a related, non-focal species of interest for the amplification of orthologous polymorphic loci; when successful, this approach significantly reduces cost and time of microsatellite development. However, transferability of polymorphic microsatellite loci decreases rapidly with increasing evolutionary distance, and this approach has shown its limits. Whole genome sequences represent an under-exploited resource to develop cross-species primers for microsatellites. Here we describe a three-step method that combines a novel in silico pipeline that we use to (1 identify conserved microsatellite loci from a multiple genome alignments, (2 design degenerate primer pairs, with (3 a simple PCR protocol used to implement these primers across species. Using this approach we developed a set of primers for the mammalian clade. We found 126,306 human microsatellites conserved in mammalian aligned sequences, and isolated 5,596 loci using criteria based on wide conservation. From a random subset of ~1000 dinucleotide repeats, we designed degenerate primer pairs for 19 loci, of which five produced polymorphic fragments in up to 18 mammalian species, including the distinctly related marsupials and monotremes, groups that diverged from other mammals 120-160 million years ago. Using our method, many more cross-clade microsatellite loci can be harvested from the currently available genomic data, and this ability is set to improve exponentially as further genomes are sequenced.

  12. Isolation and Characterization of 20 Polymorphic Microsatellite Markers for Juglans mandshurica (Juglandaceae

    Directory of Open Access Journals (Sweden)

    Chang-Mei Chen

    2013-06-01

    Full Text Available Premise of the study: Fifty microsatellite loci were developed for the endangered species Juglans mandshurica to investigate its genetic diversity and population structure. Methods and Results: In all, 50 microsatellite markers were isolated from J. mandshurica, using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO protocol. Twenty of these polymorphic markers were assessed in samples collected from 98 individuals among five populations in northeastern China. Across all of the J. mandshurica samples, the number of alleles per locus ranged from one to 17. Conclusions: These new microsatellite loci will be useful for conservation genetics studies of J. mandshurica.

  13. Isolation and characterization of microsatellite markers from the phytopathogenic fungus Alternaria dauci.

    Science.gov (United States)

    Benichou, Soumaya; Dongo, Anita; Henni, Djamel Eddine; Peltier, Didier; Simoneau, Philippe

    2009-01-01

    Eleven polymorphic microsatellite markers were isolated from the necrotrophic phytopathogenic fungus Alternaria dauci based on enriched genomic libraries. In order to assess allelic variability, the microsatellite loci were analysed in a collection of 43 isolates. The number of detected alleles in 11 loci ranged from two to 24 (mean 10.4). Test of cross-species amplification and sequencing of the resulting amplicons showed that some of these microsatellites could be used in different species such as Alternaria solani, Alternaria bataticola and Alternaria zinniae. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

  14. Development of a novel set of microsatellite markers for castor bean, Ricinus communis (Euphorbiaceae).

    Science.gov (United States)

    Bajay, Miklos Maximiliano; Zucchi, Maria Imaculada; Kiihl, Tammy Aparecida Manabe; Batista, Carlos Eduardo Araújo; Monteiro, Mariza; Pinheiro, José Baldin

    2011-04-01

    Microsatellite primers were developed for castor bean (Ricinus communis L.) to investigate genetic diversity and population structure, and to provide support to germplasm management. Eleven microsatellite loci were isolated using an enrichment cloning protocol and used to characterize castor bean germplasm from the collection at the Instituto Agronômico de Campinas (IAC). In a survey of 76 castor bean accessions, the investigated loci displayed polymorphism ranging from two to five alleles. The information derived from microsatellite markers led to significant gains in conserved allelic richness and provides support to the implementation of several molecular breeding strategies for castor bean.

  15. Larus Gull Microsatellite DNA Data, 2006-2009

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This data set describes nuclear microsatellite genotypes derived from eleven autosomal loci (Hg16, Hg18, Hg25, K16, Lar12, Lar19, Lar24, Lar26, Rbg13, Rbg18, and...

  16. Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences

    Science.gov (United States)

    Premise of the study: Chloroplast microsatellite loci were characterized from transcriptomes of Artocarpus (A.) altilis (breadfruit) and A. camansi (breadnut). They were tested in A. odoratissimus (terap) and A. altilis and evaluated in silico for two congeners. Methods and Results: 15 simple seque...

  17. Polymorphic microsatellite DNA markers in the penduline tit, Remiz pendulinus

    NARCIS (Netherlands)

    Meszaros, L. A.; Frauenfelder, N.; Van Der Velde, M.; Komdeur, J.; Szabad, J.

    2008-01-01

    To describe the exceptional mating system of the penduline tit, Remiz pendulinus, we aim to combine field observation records with DNA analysis based on polymorphic microsatellite DNA markers. Here we describe features of nine loci and their corresponding polymerase chain reaction primers. The obser

  18. A test of mink microsatellite markers in the ferret

    DEFF Research Database (Denmark)

    Anistoroaei, Razvan Marian; Christensen, Knud

    2006-01-01

    Short tandem repeats are a source of highly polymorphic markers in mammalian genomes. Genetic variations at these hypervariable loci is extensively used for linkage analysis and to identify individuals, and is very useful for interpopulation and interspecies studies. Fifty-nine microsatellite...

  19. Development and Characterization of Microsatellite Markers for Lilium longiflorum (Liliaceae

    Directory of Open Access Journals (Sweden)

    Satomi Sakazono

    2013-09-01

    Full Text Available Premise of the study: Ten microsatellite primers were developed to obtain information on genetic variation in Lilium longiflorum, a bulbous species showing high intraspecific genetic differentiation. Methods and Results: Of 61 microsatellite loci isolated using the dual suppression PCR technique, 10 loci were effective to characterize and estimate genetic variation in two populations of L. longiflorum. The number of alleles at each locus was different between the populations (averages = 3.2 and 10.3 alleles per locus, and the mean observed heterozygosity values were 0.245 and 0.732. Conclusions: Our results demonstrate that there is significant genetic variation between the populations and that the microsatellite markers developed in this study will be useful tools for the investigation of the genetic structure and mating system of natural L. longiflorum populations.

  20. Preliminary Study on Applicability of Microsatellite DNA Primers from Parasite Protozoa Trypanosoma cruzi in Free-living Protozoa

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wenjing; YU Yuhe; SHEN Yunfen; MIAO Wei; FENG Weisong

    2004-01-01

    In this paper, we took the lead in studying on specificity of the microsatellite DNA loci and applicability of microsatellite DNA primers in protozoa. In order to study characters of microsatellites in free-living protozoa, eight microsatellite loci primers developed from Trypanosoma cruzi (MCLE01, SCLE10, MCLE08, SCLE11, MCLF10, MCLG10,MCL03, MCL05) were employed to amplify microsatellite in four free-living protozoa, including Bodo designis, Euglena gracilis FACHB848, Paramecium bruzise and Tetrahymena thermophila BF1. In the amplification systems of P. bruzise, four loci (SCLE10, SCLE1 1, MCLF10, MCL03) were amplified successfully, and four amplification fragments were in proper size. In genome of E. gracilis FACHB848, five of eight primers brought five clear amplification bands. In B. designis, three (No.4, 5 and 7) of eight loci produced clear and sharp products without stutter bands, whereas no bands appeared in T.thermophila BF1. Further, eight 300-500bp amplification fragments were cloned and sequenced. Nevertheless, all sequenced products did not contain corresponding microsatellite sequence, although Bodo is in the same order and has the nearest phylogenetic relation with Trypanosoma among these four species. Thus, the microsatellite DNA primers can not be applied among order or more far taxa, and the specificity of microsatellite DNA is very high in protozoa. The results of this study will contribute to our understanding of microsatellite DNA in protozoa.

  1. Preliminary study on applicability of microsatellite DNA primers from parasite protozoa Trypanosoma cruzi in free-living protozoa

    Science.gov (United States)

    Zhang, Wenjing; Yu, Yuhe; Shen, Yunfen; Miao, Wei; Feng, Weisong

    2004-04-01

    In this paper, we took the lead in studying on specificity of the microsatellite DNA loci and applicability of microsatellite DNA primers in protozoa. In order to study characters of microsatellites in free-living protozoa, eight microsatellite loci primers developed from Trypanosoma cruzi (MCLE01, SCLE10, MCLE08, SCLE11, MCLF10, MCLG10, MCL03, MCL05) were employed to amplify microsatellite in four free-living protozoa, including Bodo designis, Euglena gracilis FACHB848, Paramecium bruzise and Tetrahymena thermophila BF1. In the amplification systems of P. bruzise, four loci (SCLE10, SCLE11, MCLF10, MCL03) were amplified successfully, and four amplification fragments were in proper size. In genome of E. gracilis FACHB848, five of eight primers brought five clear amplification bands. In B. designis, three (No.4, 5 and 7) of eight loci produced clear and sharp products without stutter bands, whereas no bands appeared in T. thermophila BF1. Further, eight 300 500 bp amplification fragments were cloned and sequenced. Nevertheless, all sequenced products did not contain corresponding microsatellite sequence, although Bodo is in the same order and has the nearest phylogenetic relation with Trypanosoma among these four species. Thus, the microsatellite DNA primers can not be applied among order or more far taxa, and the specificity of microsatellite DNA is very high in protozoa. The results of this study will contribute to our understanding of microsatellite DNA in protozoa.

  2. Comparative genome-wide polymorphic microsatellite markers in Antarctic penguins through next generation sequencing.

    Science.gov (United States)

    Vianna, Juliana A; Noll, Daly; Mura-Jornet, Isidora; Valenzuela-Guerra, Paulina; González-Acuña, Daniel; Navarro, Cristell; Loyola, David E; Dantas, Gisele P M

    Microsatellites are valuable molecular markers for evolutionary and ecological studies. Next generation sequencing is responsible for the increasing number of microsatellites for non-model species. Penguins of the Pygoscelis genus are comprised of three species: Adélie (P. adeliae), Chinstrap (P. antarcticus) and Gentoo penguin (P. papua), all distributed around Antarctica and the sub-Antarctic. The species have been affected differently by climate change, and the use of microsatellite markers will be crucial to monitor population dynamics. We characterized a large set of genome-wide microsatellites and evaluated polymorphisms in all three species. SOLiD reads were generated from the libraries of each species, identifying a large amount of microsatellite loci: 33,677, 35,265 and 42,057 for P. adeliae, P. antarcticus and P. papua, respectively. A large number of dinucleotide (66,139), trinucleotide (29,490) and tetranucleotide (11,849) microsatellites are described. Microsatellite abundance, diversity and orthology were characterized in penguin genomes. We evaluated polymorphisms in 170 tetranucleotide loci, obtaining 34 polymorphic loci in at least one species and 15 polymorphic loci in all three species, which allow to perform comparative studies. Polymorphic markers presented here enable a number of ecological, population, individual identification, parentage and evolutionary studies of Pygoscelis, with potential use in other penguin species.

  3. Development of microsatellite markers for six Tetranychus species by transfer from Tetranychus urticae genome.

    Science.gov (United States)

    Zhang, Jia; Sun, Jing-Tao; Jin, Peng-Yu; Hong, Xiao-Yue

    2016-09-01

    Microsatellite markers are frequently used to explore the population genetic structure of organisms. Spider mites (genus Tetranychus) are important agricultural pests. Several markers have been developed for T. urticae, but for other spider mites, few such markers are available, hampering studies of their population genetics. In this study, we developed and characterized microsatellite markers for six non-model spider mite species (T. truncatus, T. kanzawai, T. ludeni, T. piercei, T. phaselus and T. pueraricola) by cross-species amplification of markers in the T. urticae genome, in order to better understand the population structure of Tetranychus species. Among 228 screened loci, many were polymorphic, including 13 loci in T. urticae, 11 loci in T. truncatus, 15 loci in T. pueraricola, 23 loci in T. kanzawai, 19 loci in T. piercei, 11 loci in T. phaselus and 9 loci in T. ludeni. Sequence analysis determined that the fragment length variations of the transferred microsatellites were mainly due to the variations of the numbers of repeats. These new microsatellite markers should be useful for studying the population genetics of the seven Tetranychus species.

  4. Development of highly variable microsatellite markers for the tetraploid Silene stellata (Caryophyllaceae)1

    Science.gov (United States)

    Zhou, Juannan; Dudash, Michele R.; Fenster, Charles B.; Zimmer, Elizabeth A.

    2016-01-01

    Premise of the study: We designed and tested microsatellite markers for the North American native species Silene stellata (Caryophyllaceae) to investigate its population genetic structure and identify selection on floral design through male reproductive success. Methods and Results: A total of 153 candidate microsatellite loci were isolated based on next-generation sequencing. We identified 18 polymorphic microsatellite loci in three populations of S. stellata, with di- or trinucleotide repeats. Genotyping results showed the number of alleles per locus ranged from six to 45 and expected heterozygosity ranged from 0.511 to 0.951. Five of these loci were successfully amplified in S. virginica and S. caroliniana and were also polymorphic. Conclusions: The microsatellite markers reported here provide a valuable tool for paternity analysis in S. stellata. They will also be useful for investigating the population genetic structures of S. stellata and related species. PMID:28101439

  5. Characterization of Microsatellites in Xanthosoma sagittifolium (Araceae and Cross-Amplification in Related Species

    Directory of Open Access Journals (Sweden)

    Chloe Cathebras

    2014-06-01

    Full Text Available Premise of the study: To investigate the genetic diversity of a root crop, Xanthosoma sagittifolium, and to facilitate germplasm conservation, microsatellite loci were developed and characterized by genotyping 39 accessions from different geographic origins. Methods and Results: Using a microsatellite-enriched library approach, 17 polymorphic microsatellite markers were identified and characterized. The number of alleles for each locus ranged from two to six. Observed and expected heterozygosities ranged from 0.00 to 0.97 and from 0.09 to 0.78, respectively. Additionally, cross-amplification of these microsatellite markers was tested successfully in other species of Xanthosoma and Caladium, with rates varying from 23.5% to 100%. Conclusions: These results indicate the effectiveness of microsatellite loci developed for the characterization of X. sagittifolium genetic diversity. They are crucial for the future investigation of population dynamics and clonal identification and, therefore, for prioritizing germplasm conservation. They should also enable research on other related species.

  6. Genome-based polymorphic microsatellite development and validation in the mosquito Aedes aegypti and application to population genetics in Haiti

    Directory of Open Access Journals (Sweden)

    Streit Thomas G

    2009-12-01

    Full Text Available Abstract Background Microsatellite markers have proven useful in genetic studies in many organisms, yet microsatellite-based studies of the dengue and yellow fever vector mosquito Aedes aegypti have been limited by the number of assayable and polymorphic loci available, despite multiple independent efforts to identify them. Here we present strategies for efficient identification and development of useful microsatellites with broad coverage across the Aedes aegypti genome, development of multiplex-ready PCR groups of microsatellite loci, and validation of their utility for population analysis with field collections from Haiti. Results From 79 putative microsatellite loci representing 31 motifs identified in 42 whole genome sequence supercontig assemblies in the Aedes aegypti genome, 33 microsatellites providing genome-wide coverage amplified as single copy sequences in four lab strains, with a range of 2-6 alleles per locus. The tri-nucleotide motifs represented the majority (51% of the polymorphic single copy loci, and none of these was located within a putative open reading frame. Seven groups of 4-5 microsatellite loci each were developed for multiplex-ready PCR. Four multiplex-ready groups were used to investigate population genetics of Aedes aegypti populations sampled in Haiti. Of the 23 loci represented in these groups, 20 were polymorphic with a range of 3-24 alleles per locus (mean = 8.75. Allelic polymorphic information content varied from 0.171 to 0.867 (mean = 0.545. Most loci met Hardy-Weinberg expectations across populations and pairwise FST comparisons identified significant genetic differentiation between some populations. No evidence for genetic isolation by distance was observed. Conclusion Despite limited success in previous reports, we demonstrate that the Aedes aegypti genome is well-populated with single copy, polymorphic microsatellite loci that can be uncovered using the strategy developed here for rapid and efficient

  7. The Twelve Hotel, Barna : Video

    OpenAIRE

    Irish Food Channel

    2014-01-01

    Fergus O'Halloran, Managing Director of The Twelve Hotel in Barna in County Galway, talks about his philosophy in running this unique boutique hotel. Reproduced with kind permission from John & Sally McKenna. 3.35 mins

  8. Microsatellites for Oenothera gayleana and O. hartwegii subsp. filifolia (Onagraceae), and their utility in section Calylophus1

    Science.gov (United States)

    Lewis, Emily M.; Fant, Jeremie B.; Moore, Michael J.; Hastings, Amy P.; Larson, Erica L.; Agrawal, Anurag A.; Skogen, Krissa A.

    2016-01-01

    Premise of the study: Eleven nuclear and four plastid microsatellite markers were screened for two gypsum endemic species, Oenothera gayleana and O. hartwegii subsp. filifolia, and tested for cross-amplification in the remaining 11 taxa within Oenothera sect. Calylophus (Onagraceae). Methods and Results: Microsatellite markers were tested in two to three populations spanning the ranges of both O. gayleana and O. hartwegii subsp. filifolia. The nuclear microsatellite loci consisted of both di- and trinucleotide repeats with one to 17 alleles per population. Several loci showed significant deviation from Hardy–Weinberg equilibrium, which may be evidence of chromosomal rings. The plastid microsatellite markers identified one to seven haplotypes per population. The transferability of these markers was confirmed in all 11 taxa within Oenothera sect. Calylophus. Conclusions: The microsatellite loci characterized here are the first developed and tested in Oenothera sect. Calylophus. These markers will be used to assess whether pollinator foraging distance influences population genetic parameters in predictable ways. PMID:26949578

  9. Population structure and genetic diversity of Brazilian popcorn germplasm inferred by microsatellite markers

    Directory of Open Access Journals (Sweden)

    Tereza Aparecida da Silva

    2015-05-01

    Conclusions: The analysis allowed to identify microsatellite loci with high levels of heterozygosity (UMC1549 and UMC1072. These loci can be indicated as promising for detecting polymorphisms in popcorn accessions and in the monitoring of genetic improvement programs. Moreover, allowed to identify heterozygous accessions (BOZM 260, this accession showed allelic variation at all analyzed microsatellite loci and can be recommended for crosses with plants that have desirable agronomic characteristics, with a view to the broadening of the genetic base of popcorn accessions and developing new cultivars.

  10. Isolation and Characterization of Microsatellite Markers for Shorea platyclados (Dipterocarpaceae

    Directory of Open Access Journals (Sweden)

    Chin Hong Ng

    2013-06-01

    Full Text Available Premise of the study: Microsatellite markers were isolated and characterized in Shorea platyclados (Dipterocarpaceae for DNA profiling and genetic diversity assessment of this tropical timber species. Methods and Results: Fifteen polymorphic microsatellite loci were developed and characterized in S. platyclados using a genomic library enriched for dinucleotide (CT repeats. The primers amplified dinucleotide repeats with 3–14 alleles per locus across four natural populations. The observed and expected heterozygosities ranged from 0.292 to 1.000 and from 0.301 to 0.894, respectively. No significant deviation from Hardy–Weinberg equilibrium was detected in the 15 loci. Four loci pairs displayed linkage disequilibrium. Conclusions: These highly polymorphic markers are adequate for DNA profiling and studies of population genetics in S. platyclados.

  11. Development of Microsatellite Markers for Isodon longitubus (Lamiaceae

    Directory of Open Access Journals (Sweden)

    Tadashi Yamashiro

    2013-10-01

    Full Text Available Premise of the study: Microsatellite markers were developed for Isodon longitubus to study the natural hybridization of the species and its congeners. Methods and Results: A total of 10 primer sets were developed for I. longitubus. From the initial screening, all of 10 loci were polymorphic with five to 19 alleles per locus in the Mt. Ishizuchi population, whereas nine loci were polymorphic with two to 12 alleles per loci in the Toon population. Although one locus was monomorphic at one population, the observed and expected heterozygosity values estimated from 34 I. longitubus samples ranged from 0.273 to 1.000 and from 0.483 to 0.918, respectively. Six primer sets could amplify all three species examined in this study (I. inflexus, I. japonicus, and I. shikokianus. Conclusions: The 10 microsatellite markers developed here will be useful in analyzing the population genetic structure of I. longitubus and in studying the natural hybridization between Isodon species.

  12. Microsatellite data analysis for population genetics.

    Science.gov (United States)

    Kim, Kyung Seok; Sappington, Thomas W

    2013-01-01

    Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of variation at selectively neutral marker loci, and microsatellites continue to be a popular choice of marker. In recent decades, software programs to estimate population genetics parameters have been developed at an increasing pace as computational science and theoretical knowledge advance. Numerous population genetics software programs are presently available to analyze microsatellite genotype data, but only a handful are commonly employed for calculating parameters such as genetic variation, genetic structure, patterns of spatial and temporal gene flow, population demography, individual population assignment, and genetic relationships within and between populations. In this chapter, we introduce statistical analyses and relevant population genetic software programs that are commonly employed in the field of population genetics and molecular ecology.

  13. Development of Microsatellite Markers for the Neotropical Vine Dalechampia scandens (Euphorbiaceae

    Directory of Open Access Journals (Sweden)

    Mohsen Falahati-Anbaran

    2013-06-01

    Full Text Available Premise of the study: Microsatellite markers were developed to assess polymorphism and level of genetic diversity in four Mexican populations of the neotropical vine Dalechampia scandens (Euphorbiaceae. Methods and Results: Thirty-seven microsatellite markers representing bi-, tri-, tetra-, and pentanucleotide microsatellite repeats were developed. In total, 166 alleles were identified across 54 individuals. The number of alleles varied from one to 11 with an average of 4.49 alleles per locus. All loci except one were highly polymorphic between populations, whereas considerably less variation was detected within populations for most loci. The average observed and expected heterozygosities across study populations ranged from 0 to 0.63 and 0 to 0.59, respectively, for individual loci, and a deviation from Hardy–Weinberg equilibrium was observed for most loci. Conclusions: The developed markers may be useful for studying genetic structure, parentage analysis, mapping, phylogeography, and cross-amplification in other closely related species of Dalechampia.

  14. Development and Characterization of Microsatellite Markers for the Endangered Amazonian Tree Aniba rosaeodora (Lauraceae

    Directory of Open Access Journals (Sweden)

    Rafael C. Angrizani

    2013-09-01

    Full Text Available Premise of the study: Microsatellite loci were isolated and characterized for Brazilian rosewood (Aniba rosaeodora, an endangered neotropical hardwood tree, to investigate population and conservation genetics of this highly valuable nontimber forest resource. Methods and Results: We used an enriched genomic library method to isolate and characterize 11 nuclear microsatellite loci for A. rosaeodora, which exhibited an average of 9.6 and 8.7 alleles per locus in two populations from central Amazonia. Mean observed and expected heterozygosities over the 11 loci were 0.604 and 0.687, and 0.807 and 0.828, respectively, in the two populations. Conclusions: The polymorphic microsatellite loci developed for A. rosaeodora showed highly informative content and can be used as a powerful tool in genetic diversity and population structure, gene flow, and mating system studies for conservation purposes.

  15. Functionally relevant microsatellites in sugarcane unigenes

    Directory of Open Access Journals (Sweden)

    Singh Nagendra K

    2010-11-01

    Full Text Available Abstract Background Unigene sequences constitute a rich source of functionally relevant microsatellites. The present study was undertaken to mine the microsatellites in the available unigene sequences of sugarcane for understanding their constitution in the expressed genic component of its complex polyploid/aneuploid genome, assessing their functional significance in silico, determining the extent of allelic diversity at the microsatellite loci and for evaluating their utility in large-scale genotyping applications in sugarcane. Results The average frequency of perfect microsatellite was 1/10.9 kb, while it was 1/44.3 kb for the long and hypervariable class I repeats. GC-rich trinucleotides coding for alanine and the GA-rich dinucleotides were the most abundant microsatellite classes. Out of 15,594 unigenes mined in the study, 767 contained microsatellite repeats and for 672 of these putative functions were determined in silico. The microsatellite repeats were found in the functional domains of proteins encoded by 364 unigenes. Its significance was assessed by establishing the structure-function relationship for the beta-amylase and protein kinase encoding unigenes having repeats in the catalytic domains. A total of 726 allelic variants (7.42 alleles per locus with different repeat lengths were captured precisely for a set of 47 fluorescent dye labeled primers in 36 sugarcane genotypes and five cereal species using the automated fragment analysis system, which suggested the utility of designed primers for rapid, large-scale and high-throughput genotyping applications in sugarcane. Pair-wise similarity ranging from 0.33 to 0.84 with an average of 0.40 revealed a broad genetic base of the Indian varieties in respect of functionally relevant regions of the large and complex sugarcane genome. Conclusion Microsatellite repeats were present in 4.92% of sugarcane unigenes, for most (87.6% of which functions were determined in silico. High level of

  16. Mutation Rate at Commonly Used Forensic STR Loci: Paternity Testing Experience

    Directory of Open Access Journals (Sweden)

    Faruk Aşıcıoğlua

    2004-01-01

    Full Text Available Paternity tests are carried out by the analysis of hypervariable short tandem repeat DNA loci. These microsatellite sequences mutate at a higher rate than that of bulk DNA. The occurrence of germline mutations at STR loci posses problems in interpretation of resulting genetic profiles. We recently analyzed 59–159 parent/child allele transfers at 13 microsatellite loci. We identified 12 mutations in 7 microsatellite loci. No mutations were occurred in other 6 loci. The highest mutation rate was observed with 5 mutations at D8S1179 locus at different alleles. The event was always single repeat related. The mutation rate was between 0 and 1.5 x 10-2 per locus per gamete per generation. The mutation event is very crucial for forensic DNA testing and accumulation of STR mutation data is extremely important for genetic profile interpretation.

  17. Microsatellite markers of water buffalo, Bubalus bubalis - development, characterisation and linkage disequilibrium studies

    Directory of Open Access Journals (Sweden)

    Vaidhegi R

    2009-10-01

    Full Text Available Abstract Background Microsatellite markers are highly polymorphic and widely used in genome mapping and population genetic studies in livestock species. River buffalo, Bubalus bubalis is an economically important livestock species, though only a limited number of microsatellite markers have been reported thus far in this species. Results In the present study, using two different approaches 571 microsatellite markers have been characterized for water buffalo. Of the 571 microsatellite markers, 498 were polymorphic with average heterozygosity of 0.51 on a panel of 24 unrelated buffalo. Fisher exact test was used to detect LD between the marker pairs. Among the 137550 pairs of marker combination, 14.58% pairs showed significant LD (P Conclusion The high conservation of cattle microsatellite loci in water buffalo promises the usefulness of the cattle microsatellites markers on buffalo. The polymorphic markers characterised in this study will contribute to genetic linkage and radiation hybrid mapping of water buffalo and population genetic studies.

  18. Genotyping of mature trees of Entandrophragma cylindricum with microsatellites.

    Science.gov (United States)

    Garcia, F; Noyer, J-L; Risterucci, A-M; Chevallier, M-H

    2004-01-01

    We have characterized 10 microsatellite loci for the tropical tree Entandrophragma cylindricum (Sprague) Sprague (sapelli) in order to genotype individuals in forest stands for estimation of the genetic diversity of the species. We used the technique of building a (GA)n microsatellite-enriched library by capture with streptavidin-coated magnetic beads. We assessed the polymorphism of seven microsatellites in 186 mature trees in a selectively logged stand (Dimako) and an unlogged stand (Ndama), both in Cameroon. All the loci were polymorphic, and the number of alleles was high, ranging from eight to 36, with a mean of 22.1. Both stands showed the same high level of genetic diversity (mean H(E) = 0.85) and a low genetic differentiation (FST = 0.007), indicating that genetic diversity was within rather than among populations. Five and three out seven loci in Dimako and Ndama, respectively, showed a deficit of heterozygotes. The seven loci enabled more than 97% of the mature trees in each stand to be identified. It was concluded that these markers can be efficiently used for gene flow studies.

  19. Multi-ethnic fine-mapping of 14 central adiposity loci

    DEFF Research Database (Denmark)

    Liu, Ching-Ti; Buchkovich, Martin L; Winkler, Thomas W;

    2014-01-01

    The Genetic Investigation of Anthropometric Traits (GIANT) consortium identified 14 loci in European Ancestry (EA) individuals associated with waist-to-hip ratio (WHR) adjusted for body mass index. These loci are wide and narrowing the signals remains necessary. Twelve of 14 loci identified in GI...

  20. Genome-wide microsatellite identification in the fungus Anisogramma anomala using Illumina sequencing and genome assembly.

    Directory of Open Access Journals (Sweden)

    Guohong Cai

    Full Text Available High-throughput sequencing has been dramatically accelerating the discovery of microsatellite markers (also known as Simple Sequence Repeats. Both 454 and Illumina reads have been used directly in microsatellite discovery and primer design (the "Seq-to-SSR" approach. However, constraints of this approach include: 1 many microsatellite-containing reads do not have sufficient flanking sequences to allow primer design, and 2 difficulties in removing microsatellite loci residing in longer, repetitive regions. In the current study, we applied the novel "Seq-Assembly-SSR" approach to overcome these constraints in Anisogramma anomala. In our approach, Illumina reads were first assembled into a draft genome, and the latter was then used in microsatellite discovery. A. anomala is an obligate biotrophic ascomycete that causes eastern filbert blight disease of commercial European hazelnut. Little is known about its population structure or diversity. Approximately 26 M 146 bp Illumina reads were generated from a paired-end library of a fungal strain from Oregon. The reads were assembled into a draft genome of 333 Mb (excluding gaps, with contig N50 of 10,384 bp and scaffold N50 of 32,987 bp. A bioinformatics pipeline identified 46,677 microsatellite motifs at 44,247 loci, including 2,430 compound loci. Primers were successfully designed for 42,923 loci (97%. After removing 2,886 loci close to assembly gaps and 676 loci in repetitive regions, a genome-wide microsatellite database of 39,361 loci was generated for the fungus. In experimental screening of 236 loci using four geographically representative strains, 228 (96.6% were successfully amplified and 214 (90.7% produced single PCR products. Twenty-three (9.7% were found to be perfect polymorphic loci. A small-scale population study using 11 polymorphic loci revealed considerable gene diversity. Clustering analysis grouped isolates of this fungus into two clades in accordance with their geographic origins

  1. Genome-wide microsatellite identification in the fungus Anisogramma anomala using Illumina sequencing and genome assembly.

    Science.gov (United States)

    Cai, Guohong; Leadbetter, Clayton W; Muehlbauer, Megan F; Molnar, Thomas J; Hillman, Bradley I

    2013-01-01

    High-throughput sequencing has been dramatically accelerating the discovery of microsatellite markers (also known as Simple Sequence Repeats). Both 454 and Illumina reads have been used directly in microsatellite discovery and primer design (the "Seq-to-SSR" approach). However, constraints of this approach include: 1) many microsatellite-containing reads do not have sufficient flanking sequences to allow primer design, and 2) difficulties in removing microsatellite loci residing in longer, repetitive regions. In the current study, we applied the novel "Seq-Assembly-SSR" approach to overcome these constraints in Anisogramma anomala. In our approach, Illumina reads were first assembled into a draft genome, and the latter was then used in microsatellite discovery. A. anomala is an obligate biotrophic ascomycete that causes eastern filbert blight disease of commercial European hazelnut. Little is known about its population structure or diversity. Approximately 26 M 146 bp Illumina reads were generated from a paired-end library of a fungal strain from Oregon. The reads were assembled into a draft genome of 333 Mb (excluding gaps), with contig N50 of 10,384 bp and scaffold N50 of 32,987 bp. A bioinformatics pipeline identified 46,677 microsatellite motifs at 44,247 loci, including 2,430 compound loci. Primers were successfully designed for 42,923 loci (97%). After removing 2,886 loci close to assembly gaps and 676 loci in repetitive regions, a genome-wide microsatellite database of 39,361 loci was generated for the fungus. In experimental screening of 236 loci using four geographically representative strains, 228 (96.6%) were successfully amplified and 214 (90.7%) produced single PCR products. Twenty-three (9.7%) were found to be perfect polymorphic loci. A small-scale population study using 11 polymorphic loci revealed considerable gene diversity. Clustering analysis grouped isolates of this fungus into two clades in accordance with their geographic origins. Thus, the

  2. Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae).

    Science.gov (United States)

    Bonatelli, Isabel A S; Carstens, Bryan C; Moraes, Evandro M

    2015-01-01

    Microsatellite markers (also known as SSRs, Simple Sequence Repeats) are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq) on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms.

  3. Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae.

    Directory of Open Access Journals (Sweden)

    Isabel A S Bonatelli

    Full Text Available Microsatellite markers (also known as SSRs, Simple Sequence Repeats are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms.

  4. Mutation rate analysis at 19 autosomal microsatellites.

    Science.gov (United States)

    Qian, Xiao-Qin; Yin, Cai-Yong; Ji, Qiang; Li, Kai; Fan, Han-Ting; Yu, Yan-Fang; Bu, Fan-Li; Hu, Ling-Li; Wang, Jian-Wen; Mu, Hao-Fang; Haigh, Steven; Chen, Feng

    2015-07-01

    Previous studies have demonstrated that a large sample size is needed to reliably estimate population- and locus-specific microsatellite mutation rates. Therefore, we conducted a long-term collaboration study and performed a comprehensive analysis on the mutation characteristics of 19 autosomal short tandem repeat (STR) loci. The STR loci located on 15 of 22 autosomal chromosomes were analyzed in a total of 21,106 samples (11,468 parent-child meioses) in a Chinese population. This provided 217,892 allele transfers at 19 STR loci. An overall mutation rate of 1.20 × 10(-3) (95% CI, 1.06-1.36 × 10(-3) ) was observed in the populations across 18 of 19 STR loci, except for the TH01 locus with no mutation found. Most STR mutations (97.7%) were single-step mutations, and only a few mutations (2.30%) comprised two and multiple steps. Interestingly, approximately 93% of mutation events occur in the male germline. The mutation ratios increased with the paternal age at child birth (r = 0.99, ptesting, kinship analysis, and population genetics.

  5. Microsatellite primers for the rare sedge Lepidosperma bungalbin (Cyperaceae)1

    Science.gov (United States)

    Nevill, Paul G.; Wardell-Johnson, Grant

    2016-01-01

    Premise of the study: Microsatellite markers were developed for the rare sedge Lepidosperma bungalbin (Cyperaceae) to assess genetic variation and its spatial structuring. Methods and Results: We conducted shotgun sequencing on an Illumina MiSeq and produced 6,215,872 sequence reads. The QDD pipeline was used to design 60 primer pairs that were screened using PCR. We developed 17 loci, of which 12 loci were identified that were polymorphic, amplified reliably, and could be consistently scored. We then screened these loci for variation in individuals from three populations. The number of alleles observed for these 12 loci across the three populations ranged from nine to 19 and expected heterozygosity ranged from 0.41 to 0.89. Conclusions: These markers will enable the quantification of the potential impact of mining on genetic variation within L. bungalbin and establish a baseline for future management of genetic variation of the rare sedge. PMID:27843727

  6. Development of new microsatellite markers from Mango (Mangifera indica) and cross-species amplification.

    Science.gov (United States)

    Ravishankar, Kundapura Venkataramana; Mani, Bellam Hanumantha-Reddy; Anand, Lalitha; Dinesh, Makki Ramachandra

    2011-04-01

    Microsatellite markers were developed and characterized to assess the genetic diversity among mango (Mangifera indica) cultivars and to test their amplification in closely related species. Thirty-six microsatellite (simple sequence repeats; SSR) loci were isolated by a microsatellite-enriched partial genomic library method. Primers designed for these loci were characterized using 30 diverse mango cultivars. The number of alleles ranged from 3 to 19 with an average of 9.2 alleles per locus. Polymorphic information content values ranged from 0.185 to 0.920 with a mean of 0.687. The total value for the probability of identity was 2.42 × 10(-31). The newly identified SSRs would be useful in genetic diversity studies, finger-printing, and mapping. Loci from five related species, M. odorata, M. anadamanica, M. zeylanica, M. camptosperma, and M. griffithii, were successfully amplified using these SSR primers, showing their potential utility across species.

  7. Isolation of microsatellite primers for Melampyrum sylvaticum (Orobanchaceae), an endangered plant in the United Kingdom.

    Science.gov (United States)

    Crichton, Rhiannon J; Squirrell, Jane; Woodin, Sarah J; Dalrymple, Sarah E; Hollingsworth, Peter M

    2012-11-01

    Microsatellite markers were developed for the hemiparasitic plant Melampyrum sylvaticum to investigate the breeding system, genetic diversity, and structure of populations in the United Kingdom, Sweden, and Norway. Microsatellites were isolated from genomic DNA using an enrichment protocol. Twenty-nine loci were characterized in two individuals from each of 15 geographically disparate populations ("global"). Seven polymorphic loci were further characterized in one population ("local"). The number of alleles per locus ranged from two to 12 in the global sample and one to seven in the local sample. The expected heterozygosity ranged from 0-0.75, the observed heterozygosity from 0-0.1, and the inbreeding coefficient from 0.84-1 in the local sample. The results show the utility of these novel polymorphic microsatellite markers for further conservation genetic analyses. The strong deficit of heterozygosity across all loci in the local sample suggests the species may be inbreeding.

  8. Characterization of new microsatellite markers of Siganus fuscescens (Siganidae).

    Science.gov (United States)

    Li, Q H; Li, Z B; Dai, G; Chen, X J; Chen, L N; Cao, Y Y; Shangguan, J B; Ning, Y F

    2013-07-30

    Siganus fuscescens, which is a small commercially important marine fish, is wildly distributed in shallow waters throughout the tropical and subtropical Indo-Pacific and Eastern Mediterranean regions. It is part of a group known as rabbitfish. Fifteen new polymorphic microsatellite markers for S. fuscescens were identified, and 32 wild individuals were used to evaluate the degree of polymorphism of these markers. The number of alleles per locus ranged from 2 to 12, and the polymorphism information content ranged from 0.210 to 0.849. The observed and expected heterozygosities were 0.142-0.808 and 0.225-0.853, respectively. Although significant deviations from Hardy-Weinberg equilibrium were detected at 2 loci (Sf1-37-2 and Sf1-47), no significant deviations were detected at the other 13 loci. These microsatellite markers will provide a useful tool for studies on genetic diversity and differentiation of S. fuscescens.

  9. Microsatellite analysis of paternity and reproduction in Arctic grizzly bears.

    Science.gov (United States)

    Craighead, L; Paetkau, D; Reynolds, H V; Vyse, E R; Strobeck, C

    1995-01-01

    We report data from analyses of microsatellite loci of 30 grizzly bear family groups which demonstrate that each cub in a litter can be sired independently, and we derive estimates of maximum reproductive success for males, from an Arctic population in northwestern Alaska that is minimally affected by human activities. These analyses were made possible by the use of single-locus primers that amplified both of an individual's alleles at eight microsatellite loci and by detailed knowledge of maternal/offspring relationships that allowed the identification of paternal alleles. No single male was responsible for more than approximately 11% of known offspring, and no more than 49% of breeding-age males successfully bred. These data contribute to an understanding of the genetic and demographic basis of male reproductive success, which is of vital importance in the maintenance of small, isolated grizzly bear populations.

  10. Cross-species amplification and optimization of microsatellite markers for use in six Neotropical parrots.

    Science.gov (United States)

    Gebhardt, Kara J; Waits, Lisette P

    2008-07-01

    Short amplicon primers were redesigned for 17 microsatellite loci developed in St. Vincent's Amazon and six loci developed in blue-and-yellow macaw and tested using six species of Neotropical parrot. Polymorphism was observed at 12 loci in blue-and-yellow macaw, 10 in red-and-green macaw, 11 in scarlet macaw, 10 in chestnut-fronted macaw, 11 in red-bellied macaw and 16 in mealy parrot. Number of alleles per locus ranged from two to 23 and expected heterozygosity ranged from 0.05 to 0.95. The resulting multiplexed loci will be useful in evaluating genetic diversity, genetic structure and mating system in Neotropical parrots.

  11. Cross-genus amplification and characterisation of microsatellite loci ...

    African Journals Online (AJOL)

    Jennifer Lamb

    School of Biological and Conservation Sciences, New Biology Building, University of KwaZulu-Natal, University Road,. Westville .... 0.8 μl sterile water, 2.5 μl 10 X reaction buffer (Super- .... from Texas and Argentina, which are separated by a.

  12. Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline.

    Directory of Open Access Journals (Sweden)

    Iria Fernandez-Silva

    Full Text Available Microsatellites are the markers of choice for a variety of population genetic studies. The recent advent of next-generation pyrosequencing has drastically accelerated microsatellite locus discovery by providing a greater amount of DNA sequencing reads at lower costs compared to other techniques. However, laboratory testing of PCR primers targeting potential microsatellite markers remains time consuming and costly. Here we show how to reduce this workload by screening microsatellite loci via bioinformatic analyses prior to primer design. Our method emphasizes the importance of sequence quality, and we avoid loci associated with repetitive elements by screening with repetitive sequence databases available for a growing number of taxa. Testing with the Yellowstripe Goatfish Mulloidichthys flavolineatus and the marine planktonic copepod Pleuromamma xiphias we show higher success rate of primers selected by our pipeline in comparison to previous in silico microsatellite detection methodologies. Following the same pipeline, we discover and select microsatellite loci in nine additional species including fishes, sea stars, copepods and octopuses.

  13. Sequences Characterization of Microsatellite DNA Sequences in Pacific Abalone (Haliotis discus hannat)

    Institute of Scientific and Technical Information of China (English)

    LI Qi; Kijima Akihiro

    2007-01-01

    The microsatellite-enriched library was constructed using magnetic bead hybridization selection method, and the microsatellite DNA sequences were analyzed in Pacific abalone Haliotis discus hannai. Three hundred and fifty white colonies were screened using PCR-based technique, and 84 clones were identified to potentially contain microsatellite repeat motif. The 84 clones were sequenced, and 42 microsatellites and 4 minisatellites with a minimum of five repeats were found (13.1% of white colonies screened). Besides the motif of CA contained in the oligoprobe, we also found other 16 types of microsatellite repeats including a dinucleotide repeat, two tetranucleotide repeats, twelve pentanucleotide repeats and a hexanucleotide repeat. According to Weber(1990), the microsatellite sequences obtained could be categorized structurally into perfect repeats (73.3%), imperfect repeats(13.3%), and compound repeats (13.4%). Among the microsatellite repeats, relatively short arrays (< 20 repeats) were most abundant,accounting for 75.0%. The largest length of microsatellites was 48 repeats, and the average number of repeats was 13.4. The data on the composition and length distribution of microsatellites obtained in the present study can be useful for choosing the repeat motifs for microsatetlite isolation in other abalone species.

  14. Isolation and characterization of 29 microsatellite markers for the bumphead parrotfish, Bolbometopon muricatum, and cross amplification in 12 related species

    KAUST Repository

    Priest, Mark

    2014-10-14

    We isolated and characterized 29 microsatellite loci for the bumphead parrotfish, Bolbometopon muricatum, a wide-ranging parrotfish listed as vulnerable by the International Union for Conservation of Nature (IUCN). The 29 loci were tested on 95 individuals sampled from the Solomon Islands. The number of alleles ranged from two to ten. Evidence of linkage disequilibrium was found for only one pair of loci (Bm54 and Bm112). Two loci (Bm20 and Bm119) showed significant departure from Hardy-Weinberg equilibrium. We also tested each locus for amplification and polymorphism on 11 other scarine labrid species and one labrid species. Amplification success ranged from zero to ten loci per species. These microsatellite loci are the first specific set for B. muricatum and will be a useful tool for assessing genetic population structure, genetic diversity, and parentage in future studies.

  15. Development of nine polymorphic microsatellite markers for the phytoparasitic nematode Xiphinema index, the vector of the grapevine fanleaf virus.

    Science.gov (United States)

    Villate, L; Esmenjaud, D; Coedel, S; Plantard, O

    2009-01-01

    We report isolation, characterization and cross-species amplification of nine microsatellite loci from the phytoparasitic nematode Xiphinema index, the vector of grapevine fanleaf virus. Levels of polymorphism were evaluated in 62 individuals from two X. index populations. The number of alleles varies between two and 10 depending on locus and population. Observed heterozygosity on loci across both populations varied from 0.32 to 0.857 (mean 0.545). The primers were tested for cross-species amplification in three other species of phytoparasitic nematodes of the Xiphinema genus. These nine microsatellite loci constitute valuable markers for population genetics and phylogeographical studies of X. index.

  16. Polymorphic microsatellite markers in the brown seaweed Fucus vesiculosus.

    Science.gov (United States)

    Candeias, Rui; Casado-Amezúa, Pilar; Pearson, Gareth A; Serrão, Ester A; Teixeira, Sara

    2015-03-08

    Fucus vesiculosus is a brown seaweed dominant on temperate rocky shores of the northern hemisphere and, is typically distributed in the mid-upper intertidal zone. It is an external fertilizer that reproduces sexually, providing an excellent model to address conflicting theories related to mating systems and sexual selection. Microsatellite markers have been reported for several Fucus species, however the genomic libraries from where these markers have been isolated, have originated from two or more species pooled together (F. vesiculosus and F. serratus in one library; F. vesiculosus, F. serratus and Ascophyllum nodosum in a second library), or when the genomic DNA originated from only one species it was from Fucus spiralis. Although these markers cross-amplify F. vesiculosus individuals, the level of polymorphism has been low for relatedness studies. The microsatellite markers described here were obtained from an enriched genomic library, followed by 454 pyrosequencing. A total of 9 microsatellite markers were tested across 44 individuals from the North of Portugal. The mean number of alleles across loci was 8.7 and the gene diversity 0.67. The high variability displayed by these microsatellite loci should be useful for paternity analysis, assessing variance of reproductive success and in estimations of genetic variation within and between populations.

  17. Historical metal pollution in natural gudgeon populations: Inferences from allozyme, microsatellite and condition factor analysis

    Energy Technology Data Exchange (ETDEWEB)

    Knapen, Dries, E-mail: dries.knapen@ua.ac.be [University of Antwerp, Department of Biology, Ecophysiology, Biochemistry and Toxicology Research Group, Groenenborgerlaan 171, 2020 Antwerpen (Belgium); De Wolf, Hans [University of Antwerp, Department of Biology, Ecophysiology, Biochemistry and Toxicology Research Group, Groenenborgerlaan 171, 2020 Antwerpen (Belgium); Knaepkens, Guy [University of Antwerp, Department of Biology, Ethology Research Group, Universiteitsplein 1, 2610 Wilrijk (Belgium); Bervoets, Lieven [University of Antwerp, Department of Biology, Ecophysiology, Biochemistry and Toxicology Research Group, Groenenborgerlaan 171, 2020 Antwerpen (Belgium); Eens, Marcel [University of Antwerp, Department of Biology, Ethology Research Group, Universiteitsplein 1, 2610 Wilrijk (Belgium); Blust, Ronny [University of Antwerp, Department of Biology, Ecophysiology, Biochemistry and Toxicology Research Group, Groenenborgerlaan 171, 2020 Antwerpen (Belgium); Verheyen, Erik [Royal Belgian Institute of Natural Sciences, Department of Vertebrates, Molecular Laboratory, Vautierstraat 29, 1000 Brussel (Belgium)

    2009-10-19

    This study presents the results of a microsatellite and allozyme analysis on natural populations of the gudgeon (Gobio gobio) located in a pollution gradient of cadmium and zinc. Differences among contaminated and reference populations were observed at 2 allozyme loci, as well as a relationship between the fish condition factor and glucose-6-phosphate dehydrogenase genotypes, the locus that showed the largest difference in allele frequencies. The microsatellite data partly confirmed the differentiation pattern that was revealed by the allozyme survey. Our data further suggest that at least 2 microsatellite loci may be affected by natural selection. We thus illustrate that both microsatellite and allozyme loci do not necessarily behave as selectively neutral markers in polluted populations. Estimates of population differentiation can therefore be significantly different depending on which loci are being studied. Finally, these results are discussed in the light of the conservation unit concept, because microsatellites are often used to assess genetic variation in endangered natural populations and to propose measures for conservation or management.

  18. Distribution of trinucleotide microsatellites in different categories of mammalian genomic sequence: Implications for human genetic diseases

    Energy Technology Data Exchange (ETDEWEB)

    Stallings, R.L. (Univ. of Pittsburgh, PA (United States))

    1994-05-01

    The distribution of all trinucleotide microsatellite sequences in the GenBank database was surveyed to provide insight into human genetic disease syndromes that result from expansion of microsatellites. The microsatellite motif (CAG)[sub n] is one of the most abundant microsatellite motifs in human GenBank DNA sequences and is the most abundant microsatellite found in exons. This fact may explain why (CAG)[sub n] repeats are thus far the predominant microsatellites expanded in human genetic diseases. Surprisingly, (CAG)[sub n] microsatellites are excluded from intronic regions in a strand-specific fashion, possibly because of similarity to the 3[prime] consensus splice site, CAGG. A comparison of the positions of microsatellites in human vs rodent homologous sequences indicates that some arrays are not extensively conserved for long periods of time, even when they form parts of protein coding sequences. The general lack of conservation of trinucleotide repeat loci in diverse mammals indicates that animal models for some human microsatellite expansion syndromes may be difficult to find. 20 refs., 5 tabs.

  19. Establishment of paternity testing system using microsatellite markers in Chinese Holstein

    Institute of Scientific and Technical Information of China (English)

    Fei Tian; Dongxiao Sun; Yuan Zhang

    2008-01-01

    To estimate the efficiency of microsatellite markers in paternity testing among Chinese Holstein, 30 microsatellite loci were used to differentiate 330 Chinese Holstein genotypes, according to the calculation of the allele frequency, number of alleles, effective number of alleles, genetic heterozygosity, polymorphic information content (PIC), and the exclusion probability in this cattle population. The results demonstrated that the exclusion probability ranged from 0.620 in locus BM1818 to 0.265 in locus INRA005 with the average of 0.472 and 11 microsatellite markers exceeding 0.5. The combined exclusion probability of nine microsatellite markers was over 0.99. The result showed that paternity testing of Chinese Holstein was basically resolved using the nine microsatellite markers selected.

  20. Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification

    Directory of Open Access Journals (Sweden)

    Laura Taillebois

    2016-08-01

    Full Text Available Thirty-four microsatellite loci were isolated from three reef fish species; golden snapper Lutjanus johnii, blackspotted croaker Protonibea diacanthus and grass emperor Lethrinus laticaudis using a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1–1.5 million raw reads per species, we successfully obtained 10–13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the amplification of the golden snapper and the blackspotted croaker loci, as well as post-amplification pooling panels for the grass emperor loci. The microsatellites characterized in this work were tested across three locations of northern Australia. The microsatellites we developed can detect population differentiation across northern Australia and may be used for genetic structure studies and stock identification.

  1. In Silico Mining of Microsatellites in Coding Sequences of the Date Palm (Arecaceae Genome, Characterization, and Transferability

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    Frédérique Aberlenc-Bertossi

    2014-01-01

    Full Text Available Premise of the study: To complement existing sets of primarily dinucleotide microsatellite loci from noncoding sequences of date palm, we developed primers for tri- and hexanucleotide microsatellite loci identified within genes. Due to their conserved genomic locations, the primers should be useful in other palm taxa, and their utility was tested in seven other Phoenix species and in Chamaerops, Livistona, and Hyphaene. Methods and Results: Tandem repeat motifs of 3–6 bp were searched using a simple sequence repeat (SSR–pipeline package in coding portions of the date palm draft genome sequence. Fifteen loci produced highly consistent amplification, intraspecific polymorphisms, and stepwise mutation patterns. Conclusions: These microsatellite loci showed sufficient levels of variability and transferability to make them useful for population genetic, selection signature, and interspecific gene flow studies in Phoenix and other Coryphoideae genera.

  2. Isolation, characterization and amplification of simple sequence repeat loci in coffee

    Directory of Open Access Journals (Sweden)

    Marco-Aurelio Cristancho

    2008-01-01

    Full Text Available Simple sequence repeat (microsatellite loci in coffee were identified in clones isolated from enriched andrandom genomic libraries. It was shown that coffee is a plant species with low microsatellite frequency. However, the averagedistance between two loci, estimated at 127kb for poly (AG, is one of the shortest of all plant genomes. In contrast, thedistance between two poly (AC loci, estimated at 769kb, is one of the largest in plant genomes. Coffee (ACn microsatellites arefrequently associated with other microsatellites, mainly (ATn motifs, while (AGn microsatellites are not normally associatedwith other microsatellites and have a higher number of perfect motifs. Dinucleotide repeats (AG and (AC were found in ATrichregions in coffee. Sequence analysis of (ACn microsatellites identified in coffee revealed the possible association of theserepeated elements with miniature inverted-repeat transposable elements (MITEs. In addition, some of the evaluated SSRmarkers produced transposon-like amplification patterns in tetraploid genotypes. Of 12 SSR markers developed, nine werepolymorphic in diploid genotypes while 5 were polymorphic in tetraploid genotypes, confirming a greater genetic diversity indiploid species.

  3. A matter of life or death: how microsatellites emerge in and vanish from the human genome.

    Science.gov (United States)

    Kelkar, Yogeshwar D; Eckert, Kristin A; Chiaromonte, Francesca; Makova, Kateryna D

    2011-12-01

    Microsatellites--tandem repeats of short DNA motifs--are abundant in the human genome and have high mutation rates. While microsatellite instability is implicated in numerous genetic diseases, the molecular processes involved in their emergence and disappearance are still not well understood. Microsatellites are hypothesized to follow a life cycle, wherein they are born and expand into adulthood, until their degradation and death. Here we identified microsatellite births/deaths in human, chimpanzee, and orangutan genomes, using macaque and marmoset as outgroups. We inferred mutations causing births/deaths based on parsimony, and investigated local genomic environments affecting them. We also studied birth/death patterns within transposable elements (Alus and L1s), coding regions, and disease-associated loci. We observed that substitutions were the predominant cause for births of short microsatellites, while insertions and deletions were important for births of longer microsatellites. Substitutions were the cause for deaths of microsatellites of virtually all lengths. AT-rich L1 sequences exhibited elevated frequency of births/deaths over their entire length, while GC-rich Alus only in their 3' poly(A) tails and middle A-stretches, with differences depending on transposable element integration timing. Births/deaths were strongly selected against in coding regions. Births/deaths occurred in genomic regions with high substitution rates, protomicrosatellite content, and L1 density, but low GC content and Alu density. The majority of the 17 disease-associated microsatellites examined are evolutionarily ancient (were acquired by the common ancestor of simians). Our genome-wide investigation of microsatellite life cycle has fundamental applications for predicting the susceptibility of birth/death of microsatellites, including many disease-causing loci.

  4. Characterization of Microsatellite Markers for Pinedrops, Pterospora andromedea (Ericaceae, from Illumina MiSeq sequencing

    Directory of Open Access Journals (Sweden)

    Lisa C. Grubisha

    2014-10-01

    Full Text Available Premise of the study: Pterospora andromedea (Ericaceae is a mycoheterotrophic plant endemic to North America with a disjunct distribution. Eastern populations are in decline compared to western populations. Microsatellite loci will allow comparison of genetic diversity in endangered to nonthreatened populations. Methods and Results: Illumina MiSeq sequencing resulted in development of 12 polymorphic microsatellite loci from 63 perfect microsatellite loci tested. One polymorphic locus was obtained from a traditional enrichment method. These 13 loci were screened across two western and two eastern populations. For western and eastern populations, respectively, number of alleles ranged from one to 10 and one to four, and observed heterozygosity ranged from 0.000 to 0.389 and 0.000 to 0.143. Conclusions: These are the first microsatellite loci developed for Pterospora. They will be useful in conservation efforts of the eastern populations and for examination of population genetic parameters at different geographic scales and comparison with mycorrhizal fungal hosts.

  5. An SNP linkage scan identifies significant Crohn's disease loci on chromosomes 13q13.3 and, in Jewish families, on 1p35.2 and 3q29.

    Science.gov (United States)

    Shugart, Y Y; Silverberg, M S; Duerr, R H; Taylor, K D; Wang, M-H; Zarfas, K; Schumm, L P; Bromfield, G; Steinhart, A H; Griffiths, A M; Kane, S V; Barmada, M M; Rotter, J I; Mei, L; Bernstein, C N; Bayless, T M; Langelier, D; Cohen, A; Bitton, A; Rioux, J D; Cho, J H; Brant, S R

    2008-03-01

    Inflammatory bowel disease (IBD) is a complex genetic disorder of two major phenotypes, Crohn's disease (CD) and ulcerative colitis (UC), with increased risk in Ashkenazi Jews. Twelve genome-wide linkage screens have identified multiple loci, but these screens have been of modest size and have used low-density microsatellite markers. We, therefore, performed a high-density single-nucleotide polymorphism (SNP) genome-wide linkage study of 993 IBD multiply affected pedigrees (25% Jewish ancestry) that contained 1709 IBD-affected relative pairs, including 919 CD-CD pairs and 312 UC-UC pairs. We identified a significant novel CD locus on chromosome 13p13.3 (peak logarithm of the odds (LOD) score=3.98) in all pedigrees, significant linkage evidence on chromosomes 1p35.1 (peak LOD score=3.5) and 3q29 (peak LOD score=3.19) in Jewish CD pedigrees, and suggestive loci for Jewish IBD on chromosome 10q22 (peak LOD score=2.57) and Jewish UC on chromosome 2q24 (peak LOD score=2.69). Nominal or greater linkage evidence was present for most previously designated IBD loci (IBD1-9), notably, IBD1 for CD families at chromosome 16q12.1 (peak LOD score=4.86) and IBD6 in non-Jewish UC families at chromosome 19p12 (peak LOD score=2.67). This study demonstrates the ability of high information content adequately powered SNP genome-wide linkage studies to identify loci not observed in multiple microsatellite-based studies in smaller cohorts.

  6. varver: a database of microsatellite variation in vertebrates.

    Science.gov (United States)

    Yashima, Akiko Sato; Innan, Hideki

    2016-10-31

    Understanding how genetic variation is maintained within a species is important in ecology, evolution, conservation and population genetics. Tremendous efforts have been made to evaluate the patterns of genetic variation in natural populations of various species. For this purpose, microsatellites have played a major role since the 1990s. Here we describe a comprehensive database, varver (Variation in Vertebrates) that provides complete information regarding microsatellite variation in natural populations of vertebrates. For each species, varver includes basic information of the species, a list of publications reporting the microsatellite variation, and tables of genetic variation within and between populations (heterozygosity and FST ). The geographic location and rough sampling range are also shown for each sampled population. The database should be useful for researchers interested in not only specific species but also comparing multiple species. We discuss the utility of microsatellite data, particularly for meta-analyses that involve multiple microsatellite loci from various species. We show that in such analyses, it is extremely important to correct for biases caused by differences in mutation rate, mainly due to repeat unit and number.

  7. A novel approach for characterizing microsatellite instability in cancer cells.

    Directory of Open Access Journals (Sweden)

    Yuheng Lu

    Full Text Available Microsatellite instability (MSI is characterized by the expansion or contraction of DNA repeat tracts as a consequence of DNA mismatch repair deficiency (MMRD. Accurate detection of MSI in cancer cells is important since MSI is associated with several cancer subtypes and can help inform therapeutic decisions. Although experimental assays have been developed to detect MSI, they typically depend on a small number of known microsatellite loci or mismatch repair genes and have limited reliability. Here, we report a novel genome-wide approach for MSI detection based on the global detection of insertions and deletions (indels in microsatellites found in expressed genes. Our large-scale analyses of 20 cancer cell lines and 123 normal individuals revealed striking indel features associated with MSI: there is a significant increase of short microsatellite deletions in MSI samples compared to microsatellite stable (MSS ones, suggesting a mechanistic bias of repair efficiency between insertions and deletions in normal human cells. By incorporating this observation into our MSI scoring metric, we show that our approach can correctly distinguish between MSI and MSS cancer cell lines. Moreover, when we applied this approach to primal tumor samples, our metric is also well consistent with diagnosed MSI status. Thus, our study offers new insight into DNA mismatch repair system, and also provides a novel MSI diagnosis method for clinical oncology with better reliability.

  8. Development of microsatellite markers in Garcinia paucinervis (Clusiaceae), an endangered species of karst habitats.

    Science.gov (United States)

    Hu, Gang; Zhang, Zhong-Hua; Yang, Ping; Zhang, Qi-Wei; Yuan, Chang-An

    2017-01-01

    Microsatellite markers were developed for Garcinia paucinervis (Clusiaceae), an endangered and endemic tree species of karst habitats, to analyze its genetic diversity and genetic structure. Using shotgun sequencing on an Illumina MiSeq platform, a total of 22 microsatellite primer sets were characterized, of which 17 were identified as polymorphic. For these polymorphic loci, the total number of alleles per locus ranged from two to 12 across 54 individuals from three populations. The observed and expected heterozygosities ranged from 0.000 to 1.000 and from 0.000 to 0.850, respectively. No pair of loci showed significant linkage disequilibrium. Three loci in one population deviated significantly from Hardy-Weinberg equilibrium (P < 0.05). Seven loci (JSL3, JSL5, JSL22, JSL29, JSL32, JSL39, and JSL43) were successfully amplified in G. bracteata. These markers will be useful in studies on genetic diversity and population structure of G. paucinervis.

  9. Informative microsatellites for genetic population studies of black-faced lion tamarins (Leontopithecus caissara).

    Science.gov (United States)

    Martins, Milene Moura; Galetti, Pedro Manoel

    2011-01-01

    Leontopithecus caissara is a critically endangered primate species from the Brazilian Atlantic Forest. Nineteen microsatellite loci, previously developed for congeneric species, were tested with 34 L. caissara individuals from Superagüi Island. Of the 19 loci, 17 (89.4%) produced robust alleles, nine (47.4%) of these proved to be polymorphic, with a total of 23 alleles and an average of 2.56 alleles per locus. Expected and observed heterozygosity averaged 0.483 and 0.561, respectively. The exclusion power for identifying the first parent of an arbitrary offspring was 0.315 over all loci. The results thus indicate both the usefulness and limitations of these nine microsatellite loci in the genetic analysis of L. caissara, as well as their potentiality for genetic investigation in other congeneric species.

  10. Informative microsatellites for genetic population studies of black-faced lion tamarins (Leontopithecus caissara

    Directory of Open Access Journals (Sweden)

    Milene Moura Martins

    2011-01-01

    Full Text Available Leontopithecus caissara is a critically endangered primate species from the Brazilian Atlantic Forest. Nineteen microsatellite loci, previously developed for congeneric species, were tested with 34 L. caissara individuals from Superagüi Island. Of the 19 loci, 17 (89.4% produced robust alleles, nine (47.4% of these proved to be polymorphic, with a total of 23 alleles and an average of 2.56 alleles per locus. Expected and observed heterozygosity averaged 0.483 and 0.561, respectively. The exclusion power for identifying the first parent of an arbitrary offspring was 0.315 over all loci. The results thus indicate both the usefulness and limitations of these nine microsatellite loci in the genetic analysis of L. caissara, as well as their potentiality for genetic investigation in other congeneric species.

  11. Coding Microsatellite Frameshift Mutations Accumulate in Atherosclerotic Carotid Artery Lesions: Evaluation of 26 Cases and Literature Review.

    Science.gov (United States)

    Kurz, Carolin; Hakimi, Maani; Kloor, Matthias; Grond-Ginsbach, Caspar; Gross-Weissmann, Marie-Luise; Böckler, Dittmar; von Knebel Doeberitz, Magnus; Dihlmann, Susanne

    2015-06-09

    Somatic DNA alterations are known to occur in atherosclerotic carotid artery lesions; however, their significance is unknown. The accumulation of microsatellite mutations in coding DNA regions may reflect a deficiency of the DNA mismatch repair (MMR) system. Alternatively, accumulation of these coding microsatellite mutations may indicate that they contribute to the pathology. To discriminate between these two possibilities, we compared the mutation frequencies in coding microsatellites (likely functionally relevant) with those in noncoding microsatellites (likely neutral). Genomic DNA was isolated from carotid endarterectomy (CEA) specimens of 26 patients undergoing carotid surgery and from 15 nonatherosclerotic control arteries. Samples were analyzed by DNA fragment analysis for instability at three noncoding (BAT25, BAT26, CAT25) and five coding (AIM2, ACVR2, BAX, CASP5, TGFBR2) microsatellite loci, with proven validity for detection of microsatellite instability in neoplasms. We found an increased frequency of coding microsatellite mutations in CEA specimens compared with control specimens (34.6 versus 0%; p = 0.0013). Five CEA specimens exhibited more than one frameshift mutation, and ACVR2 and CASP5 were affected most frequently (5/26 and 6/26). Moreover, the rate of coding microsatellite alterations (15/130) differed significantly from that of noncoding alterations (0/78) in CEA specimens (p = 0.0013). In control arteries, no microsatellite alterations were observed, neither in coding nor in noncoding microsatellite loci. In conclusion, the specific accumulation of coding mutations suggests that these mutations play a role in the pathogenesis of atherosclerotic carotid lesions, since the absence of mutations in noncoding microsatellites argues against general microsatellite instability, reflecting MMR deficiency.

  12. Characterization and transferability of microsatellite markers of the cultivated peanut (Arachis hypogaea

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    Palmieri Dario A

    2007-02-01

    Full Text Available Abstract Background The genus Arachis includes Arachis hypogaea (cultivated peanut and wild species that are used in peanut breeding or as forage. Molecular markers have been employed in several studies of this genus, but microsatellite markers have only been used in few investigations. Microsatellites are very informative and are useful to assess genetic variability, analyze mating systems and in genetic mapping. The objectives of this study were to develop A. hypogaea microsatellite loci and to evaluate the transferability of these markers to other Arachis species. Results Thirteen loci were isolated and characterized using 16 accessions of A. hypogaea. The level of variation found in A. hypogaea using microsatellites was higher than with other markers. Cross-transferability of the markers was also high. Sequencing of the fragments amplified using the primer pair Ah11 from 17 wild Arachis species showed that almost all wild species had similar repeated sequence to the one observed in A. hypogaea. Sequence data suggested that there is no correlation between taxonomic relationship of a wild species to A. hypogaea and the number of repeats found in its microsatellite loci. Conclusion These results show that microsatellite primer pairs from A. hypogaea have multiple uses. A higher level of variation among A. hypogaea accessions can be detected using microsatellite markers in comparison to other markers, such as RFLP, RAPD and AFLP. The microsatellite primers of A. hypogaea showed a very high rate of transferability to other species of the genus. These primer pairs provide important tools to evaluate the genetic variability and to assess the mating system in Arachis species.

  13. [Aspirin suppresses microsatellite instability].

    Science.gov (United States)

    Wallinger, S; Dietmaier, W; Beyser, K; Bocker, T; Hofstädter, F; Fishel, R; Rüschoff, J

    1999-01-01

    Nonsteroidal anti-inflammatory drugs (NSAIDs) exhibit cancer preventive effects and have been shown to induce regression of adenomas in FAP patients. In order to elucidate the probable underlying mechanism, the effect of NSAIDs on mismatch repair related microsatellite instability was investigated. Six colorectal cancer cell lines all but one deficient for human mismatch repair (MMR) genes were examined for microsatellite instability (MSI) prior and after treatment with Aspirin or Sulindac. For rapid in vitro analysis of MSI a microcloning assay was developed by combining Laser microdissection and random (PEP-) PCR prior to specific MSI-PCR. Effects of NSAIDs on cell cycle and apoptosis were systematically investigated by using flow cytometry and cell-sorting. MSI frequency in cells deficient of MMR genes (hMSH2, hMLH1, hMSH6) was markedly reduced after long-term (> 10 weeks) NSAID treatment. This effect was reversible, time- and concentration dependent. However, in the hPMS2 deficient endometrial cancer cell line (HEC-1-A) the MSI phenotype kept unchanged. According to cell sorting, non-apoptotic cells were stable and apoptotic cells were unstable. These results suggest that aspirin/sulindac induces a genetic selection for microsatellite stability in a subset of MMR-deficient cells and may thus provide an effective prophylactic therapy for HNPCC related colorectal carcinomas.

  14. Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences.

    Science.gov (United States)

    Gardner, Elliot M; Laricchia, Kristen M; Murphy, Matthew; Ragone, Diane; Scheffler, Brian E; Simpson, Sheron; Williams, Evelyn W; Zerega, Nyree J C

    2015-09-01

    Chloroplast microsatellite loci were characterized from transcriptomes of Artocarpus altilis (breadfruit) and A. camansi (breadnut). They were tested in A. odoratissimus (terap) and A. altilis and evaluated in silico for two congeners. Fifteen simple sequence repeats (SSRs) were identified in chloroplast sequences from four Artocarpus transcriptome assemblies. The markers were evaluated using capillary electrophoresis in A. odoratissimus (105 accessions) and A. altilis (73). They were also evaluated in silico in A. altilis (10), A. camansi (6), and A. altilis × A. mariannensis (7) transcriptomes. All loci were polymorphic in at least one species, with all 15 polymorphic in A. camansi. Per species, average alleles per locus ranged between 2.2 and 2.5. Three loci had evidence of fragment-length homoplasy. These markers will complement existing nuclear markers by enabling confident identification of maternal and clone lines, which are often important in vegetatively propagated crops such as breadfruit.

  15. Microsatellite Markers for the Yam Bean Pachyrhizus (Fabaceae

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    Marc Delêtre

    2013-06-01

    Full Text Available Premise of the study: Microsatellite loci were developed for the understudied root crop yam bean (Pachyrhizus spp. to investigate intraspecific diversity and interspecific relationships within the genus Pachyrhizus. Methods and Results: Seventeen nuclear simple sequence repeat (SSR markers with perfect di- and trinucleotide repeats were developed from 454 pyrosequencing of SSR-enriched genomic libraries. Loci were characterized in P. ahipa and wild and cultivated populations of four closely related species. All loci successfully cross-amplified and showed high levels of polymorphism, with number of alleles ranging from three to 12 and expected heterozygosity ranging from 0.095 to 0.831 across the genus. Conclusions: By enabling rapid assessment of genetic diversity in three native neotropical crops, P. ahipa, P. erosus, and P. tuberosus, and two wild relatives, P. ferrugineus and P. panamensis, these markers will allow exploration of the genetic diversity and evolutionary history of the genus Pachyrhizus.

  16. The effects of read length, quality and quantity on microsatellite discovery and primer development: from Illumina to PacBio.

    Science.gov (United States)

    Wei, Na; Bemmels, Jordan B; Dick, Christopher W

    2014-09-01

    The advent of next-generation sequencing (NGS) technologies has transformed the way microsatellites are isolated for ecological and evolutionary investigations. Recent attempts to employ NGS for microsatellite discovery have used the 454, Illumina, and Ion Torrent platforms, but other methods including single-molecule real-time DNA sequencing (Pacific Biosciences or PacBio) remain viable alternatives. We outline a workflow from sequence quality control to microsatellite marker validation in three plant species using PacBio circular consensus sequencing (CCS). We then evaluate the performance of PacBio CCS in comparison with other NGS platforms for microsatellite isolation, through simulations that focus on variations in read length, read quantity and sequencing error rate. Although quality control of CCS reads reduced microsatellite yield by around 50%, hundreds of microsatellite loci that are expected to have improved conversion efficiency to functional markers were retrieved for each species. The simulations quantitatively validate the advantages of long reads and emphasize the detrimental effects of sequencing errors on NGS-enabled microsatellite development. In view of the continuing improvement in read length on NGS platforms, sequence quality and the corresponding strategies of quality control will become the primary factors to consider for effective microsatellite isolation. Among current options, PacBio CCS may be optimal for rapid, small-scale microsatellite development due to its flexibility in scaling sequencing effort, while platforms such as Illumina MiSeq will provide cost-efficient solutions for multispecies microsatellite projects.

  17. Clinicopathological significance of loss of heterozygosity and microsatellite instability in hepatocellular carcinoma in China

    Institute of Scientific and Technical Information of China (English)

    Shu-Hui Zhang; Wen-Ming Cong; Zhi-Hong Xian; Meng-Chao Wu

    2005-01-01

    AIM: To determine the features of microsatellite alterations and their association with clinicopathological characteristics of hepatocellular carcinoma (HCC). METHODS: Loss of heterozygosity (LOH) and microsatellite instability (MSI) of 55 microsatellite loci were detected with PCR-based microsatellite polymorphism analyses in tumors and corresponding noncancerous liver tissues of 56 surgically resected HCCs using the MegaBACE 500 automatic DNA analysis system.RESULTS: LOH was found in 44 of 56 HCCs (78.6%) at one or several loci. Frequencies of LOH on 1p, 4q, 8p,16q, and 17p were 69.6% (39/56), 71.4% (40/56), 66.1% (37/56), 66.1% (37/56), and 64.3% (36/56), respectively. MSI was found in 18 of 56 HCCs (32.1%) at one or several loci. Ten of fifty-six (17.9%) HCCs had MSI-H. Serum HBV infection, alpha-fetoprotein concentration, tumor size, cirrhosis, histological grade, tumor capsule, as well as tumor intrahepatic metastasis, might be correlated with LOH on certain chromosome regions. CONCLUSION: Frequent microsatellite alterations exist in HCC. LOH, which represents a tumor suppressor gene pathway, plays a more important role in hepatocarcinogenesis. MSI, which represents a mismatch repair genepathway, is a rare event during liver carcinogenesis. Furthermore, LOH on certain chromosome regions may be correlated with clinicopathological characteristics in HCC.

  18. Forecast of the Heterosis of Imported Meat Sheep by Genetic Polymorphism of Microsatellite DNA

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ying-jie; LIU Yue-qin; SUN Hong-xin; SUN Shao-hua; LI Yu

    2007-01-01

    Forecast of the heterosis of Small Tail Han sheep crossed with imported meat sheep by genetic polymorphism of microsatellite DNA was done in different sheep breeds. The gene frequency, the polymorphism information contents, the number of effective alleles, the heterozygosity, and the genetic distances were studied in four imported meat sheep and Small Tail Han sheep using five microsatellite loci. The crossing effects on the Small Tail Han sheep with four imported meat sheep were tested. The results indicate that there are genetic polymorphisms at five microsatellite loci in five sheep breeds. Five microsatellite loci can be used for genetic diversity evaluation in sheep breeds. The genetic variability of Dorset is the highest, and that of the Small Tail Han sheep is the lowest in the five sheep breeds. The order of heterosis from large to small in four imported meat sheep by the analysis of genetic relationship is White-Suffolk, Black-Suffolk,Dorset, and Texel. This accords with the testing results of actual heterosis. It is feasible to forecast the heterosis of Small Tail Han sheep crossed with imported meat sheep by genetic polymorphism of microsatellite DNA, which will have an important value for sheep breeding in the future.

  19. Development of novel microsatellite markers for strain-specific identification of Chlorella vulgaris.

    Science.gov (United States)

    Jo, Beom-Ho; Lee, Chang Soo; Song, Hae-Ryong; Lee, Hyung-Gwan; Oh, Hee-Mock

    2014-09-01

    A strain-specific identification method is required to secure Chlorella strains with useful genetic traits, such as a fast growth rate or high lipid productivity, for application in biofuels, functional foods, and pharmaceuticals. Microsatellite markers based on simple sequence repeats can be a useful tool for this purpose. Therefore, this study developed five novel microsatellite markers (mChl-001, mChl-002, mChl-005, mChl-011, and mChl-012) using specific loci along the chloroplast genome of Chlorella vulgaris. The microsatellite markers were characterized based on their allelic diversities among nine strains of C. vulgaris with the same 18S rRNA sequence similarity. Each microsatellite marker exhibited 2~5 polymorphic allele types, and their combinations allowed discrimination between seven of the C. vulgaris strains. The two remaining strains were distinguished using one specific interspace region between the mChl-001 and mChl-005 loci, which was composed of about 27 single nucleotide polymorphisms, 13~15 specific sequence sites, and (T)n repeat sites. Thus, the polymorphic combination of the five microsatellite markers and one specific locus facilitated a clear distinction of C. vulgaris at the strain level, suggesting that the proposed microsatellite marker system can be useful for the accurate identification and classification of C. vulgaris.

  20. Polymorphic microsatellites developed by cross-species amplifications in common pheasant breeds

    NARCIS (Netherlands)

    Baratti, M.; Alberti, A.; Groenen, M.A.M.; Veenendaal, T.; Fulgheri, F.D.

    2001-01-01

    Genetic variability was analysed in two common breeds of pheasant (Phasianus colchicus L. 1758) by means of cross-species amplifications of microsatellite loci: 154 chicken, Gallus gallus and 32 turkey, Meleagris gallopavo, primers were tested for amplification of pheasant DNA. Thirty-six primers (2

  1. Characterization and cross-amplification of microsatellite markers in four species of anemonefish (Pomacentridae, Amphiprion spp.)

    KAUST Repository

    Bonin, Mary C.

    2015-04-09

    Anemonefish are iconic symbols of coral reefs and have become model systems for research on larval dispersal and population connectivity in coral reef fishes. Here we present 24 novel microsatellite markers across four species of anemonefish and also test 35 previously published markers for cross-amplification on two anemonefish species in order to facilitate further research on their population genetics and phylogenetics. Novel loci were isolated from sequences derived from microsatellite-enriched or 454 GS-FLX shotgun sequence libraries developed using congeneric DNA. Primer testing successfully identified 15 new microsatellite loci for A. percula, 4 for A. melanopus, 3 for A. akindynos, and 2 for A. omanensis. These novel microsatellite loci were polymorphic with a mean of 10 ± 1.6 SE (standard error) alleles per locus and an average observed heterozygosity of 0.647 ± 0.032 SE. Reliable cross-amplification of 12 and 26 of the 35 previously published Amphiprion markers was achieved for A. melanopus and A. akindynos, respectively, suggesting that the use of markers developed from the DNA of congeners can provide a quick and cost-effective alternative to the isolation of new loci. Together, the markers presented here provide an important resource for ecological, evolutionary, and conservation genetic research on anemonefishes that will inform broader conservation and management actions for coral reef fishes. © 2015 Senckenberg Gesellschaft für Naturforschung and Springer-Verlag Berlin Heidelberg

  2. What phylogeny and gene genealogy analyses reveal about homoplasy in citrus microsatellite alleles

    Science.gov (United States)

    Sixty-five microsatellite alleles from three Simple Sequence Repeat (SSR) loci (cAGG9, CCT01 and GT03) of various Citrus, Fortunella or Poncirus accessions were cloned and sequenced to determine their mode of evolution. This data was used to assess sequence variation by calculating the average numb...

  3. Eleven novel polymorphic microsatellite DNA markers from the green-lipped mussel Perna viridis.

    Science.gov (United States)

    Ong, C C; Teh, C H; Tan, S G; Yusoff, K; Yap, C K

    2008-04-01

    We report on the characterization of 11 polymorphic microsatellite loci in P. viridis, the first set of such markers developed and characterized for this species. The number of alleles per locus ranged from 2 to 7, whereas the observed heterozygosity ranged from 0.0447 to 0.4837. These markers should prove useful as powerful genetic markers for this species.

  4. Temporal genetic variation as revealed by a microsatellite analysis of European sardine ( Sardina pilchardus) archived samples

    DEFF Research Database (Denmark)

    Ruggeri, Paolo; Splendiani, Andrea; Bonanomi, Sara;

    2012-01-01

    The Adriatic stock of European sardine ( Sardina pilchardus) has experienced large interannual demographic fluctuations over the last 30 years, with a severe decline beginning in 1991 and continuing until 1997. In the present study, six microsatellite loci were used on a time series collection of...

  5. Microsatellite fingerprinting in the International Cocoa Genebank, Trinidad: Accession and plot homogeneity information for germplasm management

    Science.gov (United States)

    The International Cocoa Genebank, Trinidad (ICG,T) is the largest public domain field gene bank collection of cacao and the correct identity of each tree is crucial for germplasm movement, evaluation and phenotypic characterization. Nine microsatellite loci were used to assess the identity of 1480 t...

  6. Microsatellite markers for the human nematode parasite Ascaris lumbricoides: development and assessment of utility.

    Science.gov (United States)

    Criscione, Charles D; Anderson, Joel D; Raby, Kyle; Sudimack, Dan; Subedi, Janardan; Rai, Dev R; Upadhayay, Ram P; Jha, Bharat; Williams-Blangero, Sarah; Anderson, Timothy J C

    2007-06-01

    We describe 35 microsatellite markers from the human parasitic nematode Ascaris lumbricoides. We found 7 sex-linked markers and demonstrate that 26 autosomal loci can be scored reliably. These markers have high genetic variability and provide the tools to address multiple questions concerning the epidemiology, fine-scale genetic structure, host specificity, and mating systems of this parasite.

  7. Estimating null allele frequencies at a microsatellite locus in the oystercatcher (Haematopus ostralegus)

    NARCIS (Netherlands)

    Van Treuren, R

    1998-01-01

    A significant heterozygote deficiency was found for microsatellite locus 20H7 among adult breeding birds in four populations of the oystercatcher (Haematopus ostralegus). Genotype frequencies at seven other loci were according to Hardy-Weinberg equilibria. Deviations between observed and expected ge

  8. Novel Polymorphic Microsatellite Markers Reveal Genetic Differentiation between Two Sympatric Types of Galaxea fascicularis.

    Directory of Open Access Journals (Sweden)

    Yuichi Nakajima

    Full Text Available The reef-building, scleractinian coral, Galaxea fascicularis, is classified into soft and hard types, based on nematocyst morphology. This character is correlated with the length of the mitochondrial non-coding region (mt-Long: soft colony type, and nematocysts with wide capsules and long shafts; mt-Short: hard colony type, and nematocysts with thin capsules and short shafts. We isolated and characterized novel polymorphic microsatellite markers for G. fascicularis using next-generation sequencing. Based upon the mitochondrial non-coding region, 53 of the 97 colonies collected were mt-Long (mt-L and 44 were mt-Short (mt-S. Among the 53 mt-L colonies, 27 loci were identified as amplifiable, polymorphic microsatellite loci, devoid of somatic mutations and free of scoring errors. Eleven of those 27 loci were also amplifiable and polymorphic in the 44 mt-S colonies; these 11 are cross-type microsatellite loci. The other 16 loci were considered useful only for mt-L colonies. These 27 loci identified 10 multilocus lineages (MLLs among the 53 mt-L colonies (NMLL/N = 0.189, and the 11 cross-type loci identified 7 MLLs in 44 mt-S colonies (NMLL/N = 0.159. Significant genetic differentiation between the two types was detected based on the genetic differentiation index (FST = 0.080, P = 0.001. Bayesian clustering also indicated that these two types are genetically isolated. While nuclear microsatellite genotypes also showed genetic differentiation between mitochondrial types, the mechanism of divergence is not yet clear. These markers will be useful to estimate genetic diversity, differentiation, and connectivity among populations, and to understand evolutionary processes, including divergence of types in G. fascicularis.

  9. Development of Polymorphic Microsatellite Markers for Phyllostachys edulis (Poaceae, an Important Bamboo Species in China

    Directory of Open Access Journals (Sweden)

    Wei-Xin Jiang

    2013-06-01

    Full Text Available Premise of the study: Polymorphic microsatellite markers were developed for Phyllostachys edulis (Poaceae, an ecologically and economically important bamboo species in China, to evaluate the genetic diversity and population genetic structure of P. edulis and other Phyllostachys species. Methods and Results: Twenty microsatellite markers were developed and their polymorphisms were tested on 71 samples from three geographically disparate populations. Each locus exhibited between two and 10 alleles with an average of five alleles. Excluding monomorphic loci, observed and expected heterozygosity ranged from zero to one and from 0.041 to 0.676, respectively. Conclusions: These 20 polymorphic microsatellite loci will be useful for studies on the molecular ecology, population genetics, and conservation of P. edulis.

  10. Polymorphic Microsatellite Markers for a Wind-Dispersed Tropical Tree Species, Triplaris cumingiana (Polygonaceae

    Directory of Open Access Journals (Sweden)

    Na Wei

    2014-09-01

    Full Text Available Premise of the study: Novel microsatellite markers were characterized in the wind-dispersed and dioecious neotropical tree Triplaris cumingiana (Polygonaceae for use in understanding the ecological processes and genetic impacts of pollen- and seed-mediated gene flow in tropical forests. Methods and Results: Sixty-two microsatellite primer pairs were screened, from which 12 markers showing five or more alleles per locus (range 5–17 were tested on 47 individuals. Observed and expected heterozygosities averaged 0.692 and 0.731, respectively. Polymorphism information content was between 0.417 and 0.874. Linkage disequilibrium was observed in one of the 66 pairwise comparisons between loci. Two loci showed deviation from Hardy–Weinberg equilibrium. An additional 14 markers exhibiting lower polymorphism were characterized on a smaller number of individuals. Conclusions: These microsatellite markers have high levels of polymorphism and reproducibility and will be useful in studying gene flow and population structure in T. cumingiana.

  11. Characterization of polymorphic microsatellite markers in Pinus armandii (Pinaceae), an endemic conifer species to China1

    Science.gov (United States)

    Dong, Wan-Lin; Wang, Ruo-Nan; Yan, Xiao-Hao; Niu, Chuan; Gong, Lin-Lin; Li, Zhong-Hu

    2016-01-01

    Premise of the study: Pinus armandii (Pinaceae) is an important conifer tree species in central and southwestern China, and it plays a key role in the local forest ecosystems. To investigate its population genetics and design effective conservation strategies, we characterized 18 polymorphic microsatellite markers for this species. Methods and Results: Eighteen novel polymorphic and 16 monomorphic microsatellite loci of P. armandii were isolated using Illumina MiSeq technology. The number of alleles per locus ranged from two to five. The expected heterozygosity ranged from 0.061 to 0.609 with an average of 0.384, and the observed heterozygosity ranged from 0.063 to 0.947 with an average of 0.436. Seventeen loci could be successfully transferred to five related Pinus species (P. koraiensis, P. griffithii, P. sibirica, P. pumila, and P. bungeana). Conclusions: These novel microsatellites could potentially be used to investigate the population genetics of P. armandii and related species.

  12. Evidence of multiple paternity in Morelet's Crocodile (Crocodylus moreletii) in Belize, CA, inferred from microsatellite markers.

    Science.gov (United States)

    McVay, John D; Rodriguez, David; Rainwater, Thomas R; Dever, Jennifer A; Platt, Steven G; McMurry, Scott T; Forstner, Michael R J; Densmore, Llewellyn D

    2008-12-01

    Microsatellite data were generated from hatchlings collected from ten nests of Morelet's Crocodile (Crocodylus moreletii) from New River Lagoon and Gold Button Lagoon in Belize to test for evidence of multiple paternity. Nine microsatellite loci were genotyped for 188 individuals from the 10 nests, alongside 42 nonhatchlings from Gold Button Lagoon. Then mitochondrial control region sequences were generated for the nonhatchlings and for one individual from each nest to test for presence of C. acutus-like haplotypes. Analyses of five of the nine microsatellite loci revealed evidence that progeny from five of the ten nests were sired by at least two males. These data suggest the presence of multiple paternity as a mating strategy in the true crocodiles. This information may be useful in the application of conservation and management techniques to the 12 species in this genus, most of which are threatened or endangered.

  13. Fourteen polymorphic microsatellite markers for the threatened Arnica montana (Asteraceae)1

    Science.gov (United States)

    Duwe, Virginia K.; Ismail, Sascha A.; Buser, Andres; Sossai, Esther; Borsch, Thomas; Muller, Ludo A. H.

    2015-01-01

    • Premise of the study: Microsatellite markers were developed to investigate population genetic structure in the threatened species Arnica montana. • Methods and Results: Fourteen microsatellite markers with di-, tetra-, and hexanucleotide repeat motifs were developed for A. montana using 454 pyrosequencing without and with library-enrichment methods, resulting in 56,545 sequence reads and 14,467 sequence reads, respectively. All loci showed a high level of polymorphism, with allele numbers ranging from four to 11 in five individuals from five populations (25 samples) and an expected heterozygosity ranging from 0.192 to 0.648 across the loci. • Conclusions: This set of microsatellite markers is the first one described for A. montana and will facilitate conservation genetic applications as well as the understanding of phylogeographic patterns in this species. PMID:25606354

  14. Development of microsatellite markers using Illumina MiSeq sequencing to characterize Ephedra gerardiana (Ephedraceae)1

    Science.gov (United States)

    De, Ji; Zhu, Weidong; Liu, Tianmeng; Wang, Zhe; Zhong, Yang

    2017-01-01

    Premise of the study: Ephedra gerardiana (Ephedraceae), occurring in the Himalayan ranges, is an important plant species used in Tibetan medicine. Due to the lack of molecular markers to characterize genetic diversity, knowledge for conservation and uses of E. gerardiana resources is limited; we therefore developed microsatellite markers for use in this species. Methods and Results: Using Illumina MiSeq sequencing technology, we developed 29 polymorphic microsatellite loci suitable for E. gerardiana, of which 15 loci also showed polymorphisms in two related Ephedra species, E. saxatilis and E. monosperma. The average number of effective alleles per locus ranged from two to six. The observed and expected heterozygosity ranged from 0.23 to 0.83 and 0.44 to 0.86, respectively, in E. gerardiana populations. Conclusions: The developed 29 microsatellite markers are effective for the study of genetic structure and genetic diversity of E. gerardiana, and 15 of these markers are suitable for related Ephedra species. PMID:28337389

  15. Characterization of 35 novel microsatellite DNA markers from the duck (Anas platyrhynchos genome and cross-amplification in other birds

    Directory of Open Access Journals (Sweden)

    Xu Ke

    2005-07-01

    Full Text Available Abstract In order to study duck microsatellites, we constructed a library enriched for (CAn, (CAGn, (GCCn and (TTTCn. A total of 35 pairs of primers from these microsatellites were developed and used to detect polymorphisms in 31 unrelated Peking ducks. Twenty-eight loci were polymorphic and seven loci were monomorphic. A total of 117 alleles were observed from these polymorphic microsatellite markers, which ranged from 2 to 14 with an average of 4.18 per locus. The frequencies of the 117 alleles ranged from 0.02 to 0.98. The highest heterozygosity (0.97 was observed at the CAUD019 microsatellite locus and the lowest heterozygosity (0.04 at the CAUD008 locus, and 11 loci had heterozygosities greater than 0.50 (46.43%. The polymorphism information content (PIC of 28 loci ranged from 0.04 to 0.88 with an average of 0.42. All the above markers were used to screen the polymorphism in other bird species. Two markers produced specific monomorphic products with the chicken DNA. Fourteen markers generated specific fragments with the goose DNA: 5 were polymorphic and 9 were monomorphic. But no specific product was detected with the peacock DNA. Based on sequence comparisons of the flanking sequence and repeat, we conclude that 2 chicken loci and 14 goose loci were true homologous loci of the duck loci. The microsatellite markers identified and characterized in the present study will contribute to the genetic map, quantitative traits mapping, and phylogenetic analysis in the duck and goose.

  16. 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.

  17. Microsatellite instability and cytogenetic survey in myeloid leukemias

    Directory of Open Access Journals (Sweden)

    E.M.S.F. Ribeiro

    2002-02-01

    Full Text Available Microsatellites are short tandem repeat sequences dispersed throughout the genome. Their instability at multiple genetic loci may result from mismatch repair errors and it occurs in hereditary nonpolyposis colorectal cancer. This instability is also found in many sporadic cancers. In order to evaluate the importance of this process in myeloid leukemias, we studied five loci in different chromosomes of 43 patients, 22 with chronic myelocytic leukemia (CML in the chronic phase, 7 with CML in blast crisis, and 14 with acute myeloid leukemia (AML, by comparing leukemic DNA extracted from bone marrow and constitutional DNA obtained from buccal epithelial cells. Only one of the 43 patients (2.1%, with relapsed AML, showed an alteration in the allele length at a single locus. Cytogenetic analysis was performed in order to improve the characterization of leukemic subtypes and to determine if specific chromosome aberrations were associated with the presence of microsatellite instability. Several chromosome aberrations were observed, most of them detected at diagnosis and during follow-up of the patients, according to current literature. These findings suggest that microsatellite instability is an infrequent genetic event in myeloid leukemias, adding support to the current view that the mechanisms of genomic instability in solid tumors differ from those observed in leukemias, where specific chromosome aberrations seem to play a major role.

  18. Polymorphic microsatellite DNA markers for the Florida manatee (Trichechus manatus latirostris)

    Science.gov (United States)

    Pause, K.C.; Nourisson, C.; Clark, A.; Kellogg, M.E.; Bonde, R.K.; McGuire, P.M.

    2007-01-01

    Florida manatees (Trichechus manatus latirostris) are marine mammals that inhabit the coastal waters and rivers of the southeastern USA, primarily Florida. Previous studies have shown that Florida manatees have low mitochondrial DNA variability, suggesting that nuclear DNA loci are necessary for discriminatory analyses. Here we report 10 polymorphic microsatellite loci with an average of 4.2 alleles per locus, and average heterozygosity of 50.1%. These loci have been developed for use in population studies, parentage assignment, and individual identification. ?? 2007 Blackwell Publishing Ltd.

  19. Microsatellite alterations in phenotypically normal esophageal squamous epithelium and metaplasia-dysplasia-adenocarcinoma sequence

    Institute of Scientific and Technical Information of China (English)

    Jian-Chun Cai; Di Liu; Kai-Hua Liu; Hai-Ping Zhang; Shan Zhong; Ning-Sao Xia

    2008-01-01

    AIM: To investigate the microsatellite alterations in phenotypically normal esophageal squamous epithelium and metaplasia-dysplasia-adenocarcinoma sequence.METHODS: Forty-one specimens were obtained from esophageal cancer (EC) patients. Histopathological assessment identified 23 squamous cell carcinomas (SCC) and 18 adenocarcinomas (ADC), including only 8 ADC with Barrett esophageal columnar epithelium (metaplasia) and dysplasia adjacent to ADC. Paraffinembedded normal squamous epithelium, Barrett esophageal columnar epithelium (metaplasia), dysplasia and esophageal tumor tissues were dissected from the surrounding tissues under microscopic guidance. DNA was extracted using proteinase K digestion buffer, and DNA was diluted at 1:100, 1:1000, 1:5000, 1:10000 and 1:50000, respectively. Seven microsatellite markers (D2S123, D3S1616, D3S1300, D5S346, D17S787, D18S58 and BATRII loci) were used in this study. Un-dilution and dilution polymerase chain reactions (PCR) were performed, and microsatellite analysis was carried out.RESULTS: No statistically significant difference was found in microsatellite instability (MSI) and loss of heterozygosity (LOH) of un-diluted DNA between SCC and ADC. The levels of MSI and LOH were high in the metaplasia-dysplasia-adenocarcinoma sequence of diluted DNA. The more the diluted DNA was, the higher the rates of MSI and LOH were at the above 7 loci, especially at D3S1616, D5S346, D2S123, D3S1300 and D18S58 loci.CONCLUSION: The sequence of metaplasia-dysplasia-adenocarcinoma is associated with microsatellite alterations, including MSI and LOH. The MSI and LOH may be the early genetic events during esophageal carcinogenesis, and genetic alterations at the D3S1616, D5S346 and D3S123 loci may play a role in the progress of microsatellite alterations.

  20. A new set of microsatellite markers for the peach palm (Bactris gasipaes Kunth): characterization and across-taxa utility within the tribe Cocoeae.

    NARCIS (Netherlands)

    Billotte, N.; Couvreur, T.L.P.; Marseillac, P.; Brottier, P.; Perthuis, B.; Vallejo, M.; Noyer, J.L.; Jacquemoud, J.P.; Risterucci, A.M.; Pintaud, J.C.

    2004-01-01

    A (GA)n microsatellite-enriched library was constructed and a new set of 18 nuclear simple sequence repeat loci was isolated in Bactris gasipaes var. gasipaes. The loci were found to be highly variable in the target species and readily transferable to related Bactris species as well as to the Astroc

  1. Microsatellite genotyping of carnation varieties

    NARCIS (Netherlands)

    Smulders, M.J.M.; Noordijk, Y.; Rus-Kortekaas, W.; Bredemeijer, G.M.M.; Vosman, B.

    2003-01-01

    A set of 11 sequence-tagged microsatellite markers for carnation (Dianthus caryophyllus) was developed using a DNA library enriched for microsatellites. Supplemented with three markers derived from sequence database entries, these were used to genotype carnation varieties using a semi-automated fluo

  2. Transanal rectopexy - twelve case studies

    Directory of Open Access Journals (Sweden)

    Rubens Henrique Oleques Fernandes

    2012-06-01

    Full Text Available OBJECTIVES: This study analyzed the results of transanal rectopexy and showed the benefits of this surgical technique. METHOD: Twelve patients were submitted to rectopexy between 1997 and 2011. The surgical technique used was transanal rectopexy, where the mesorectum was fixed to the sacrum with nonabsorbable suture. Three patients had been submitted to previous surgery, two by the Delorme technique and one by the Thiersch technique. RESULTS: Postoperative hospital stay ranged from 1 to 4 days. One patient (8.3% had intraoperative hematoma, which was treated with local compression and antibiotics. One patient (8.3% had residual mucosal prolapse, which was resected. Prolapse recurrence was seen in one case (8.3%. Improved incontinence occurred in 75% of patients and one patient reported obstructed evacuation in the first month after surgery. No death occurred. CONCLUSION: Transanal rectopexy is a simple, low cost technique, which has shown good efficacy in rectal prolapse control.OBJETIVO: O presente estudo analisou os resultados da retopexia pela via transanal e expôs os benefícios desta técnica cirúrgica. MÉTODO: Doze pacientes com prolapso foram operados no período de 1997 a 2011. A técnica cirúrgica usada foi a retopexia transanal, onde o mesorreto foi fixado ao sacro com fio inabsorvível. Três pacientes tinham cirurgia prévia, dois pela técnica de Delorme e um pela técnica de Thiersch. RESULTADOS: A permanência hospitalar pós-operatória variou de 1- 4 dias. Uma paciente (8,3% apresentou hematoma transoperatório que foi tratado com compressão local e antibioticoterapia. Um paciente apresentou prolapso mucoso residual (8,3%, que foi ressecado. Houve recidiva da procidência em um caso (8,3%. A melhora da incontinência ocorreu em 75% dos pacientes e uma paciente apresentou bloqueio evacuatório no primeiro mês após a cirurgia. Não houve mortalidade entre os pacientes operados. CONCLUSÃO: A retopexia transanal é uma t

  3. New Microsatellite Markers for Wild and Commercial Species of Passiflora (Passifloraceae and Cross-Amplification

    Directory of Open Access Journals (Sweden)

    Carlos B. M. Cerqueira-Silva

    2014-02-01

    Full Text Available Premise of the study: We developed the first microsatellites for Passiflora setacea and characterized new sets of markers for P. edulis and P. cincinnata, enabling further genetic diversity studies to support the conservation and breeding of passion fruit species. Methods and Results: We developed 69 microsatellite markers and, in conjunction with assessments of cross-amplification using primers available from the literature, present 43 new polymorphic microsatellite loci for three species of Passiflora. The mean number of alleles per locus was 3.1, and the mean values of the expected and observed levels of heterozygosity were 0.406 and 0.322, respectively. Conclusions: These microsatellite markers will be valuable tools for investigating the genetic diversity and population structure of wild and commercial species of passion fruit (Passiflora spp. and may be useful for developing conservation and improvement strategies by contributing to the understanding of the mating system and hybridization within the genus.

  4. Development of microsatellite markers for the clonal shrub Orixa japonica (Rutaceae) using 454 sequencing1

    Science.gov (United States)

    Tamaki, Ichiro; Setsuko, Suzuki; Sugai, Kyoko; Yanagisawa, Nao

    2016-01-01

    Premise of the study: Microsatellite markers were developed for a dioecious shrub, Orixa japonica (Rutaceae). Because O. japonica vigorously propagates by vegetative growth, microsatellite markers can be used to identify clonal relationships among its ramets. Methods and Results: Sixteen polymorphic microsatellite markers were identified by 454 next-generation sequencing. The number of alleles and expected heterozygosity for each locus among four populations ranged from two to 10 and from 0.140 to 0.875, respectively. Five of the 16 loci showed a low null allele frequency. Because Orixa is a monotypic genus, cross-amplification in a consubfamilial species, Skimmia japonica, was tested, and only one locus showed polymorphism. Conclusions: These microsatellite markers developed for O. japonica contribute to clone identification for studies examining the clonal structure and true sex ratio in the wild. Moreover, five markers that have a low null allele frequency can also be used for estimating mating systems or performing parentage analysis. PMID:27785383

  5. Microsatellite isolation and characterization for Colletotrichum spp, causal agent of anthracnose in Andean blackberry.

    Science.gov (United States)

    Marulanda, M L; López, A M; Isaza, L; López, P

    2014-09-26

    The genus Colletotrichum, comprised of pathogenic fungi that affect plants grown worldwide, causes the disease known as anthracnose in several fruit and vegetable species. Several studies conducted on plants have shown that the disease is characterized by the presence of one or several species of the fungus attacking the fruit or other organs of the same host. To develop and implement effective control strategies, it is vital to understand the genetic structure of the fungus in agricultural systems, identify associated Colletotrichum species, and define the subpopulations responsible for the disease. Molecular tools were accordingly developed to characterize genotypic populations of Colletotrichum spp, causal agent of anthracnose in commercial crops of Andean blackberry (Rubus glaucus Benth.). A microsatellite-enriched library for Colletotrichum gloeosporioides was developed to identify and characterize microsatellite loci among isolates collected in R. glaucus plantations. Thirty microsatellites were developed and tested in 36 isolates gathered from eight different blackberry-production areas of Colombia. Ten pairs of microsatellites were polymorphic.

  6. Microsatellite polymorphisms of Sichuan golden monkeys

    Institute of Scientific and Technical Information of China (English)

    PAN Deng; LI Ying; HU Hongxing; MENG Shijie; MEN Zhengrning; FU Yunxin; ZHANG Yaping

    2005-01-01

    Previous study using protein electrophoresis shows no polymorphism in 44 nuclear loci of Sichuan golden monkey (Rhinopithecus roxellana), which limits our understandings of its population genetic patterns in the nuclear genome. In order to obtain sufficient information, we scanned 14 microsatellite loci in a sample of 32 individuals from its three major habitats (Minshan, Qinling and Shennongjia). A considerable amount of polymorphisms were detected. The average heterozygosities in the local populations were all above 0.5. The differentiations among local populations were significant. There was evidence of geneflow among subpopulations, but geneflow between Qinling and Shennongjia local populations was the weakest. Minshan and Qinling populations might have gone through recent bottlenecks. The estimation of the ratio of the effective population sizes among local populations was close to that from census sizes. Comparisons to available mitochondria data suggested that R. roxellana's social structures played an important role in shaping its population genetic patterns. Our study showed that the polymorphism level of R. roxellana was no higher than other endangered species; therefore, measures should be taken to preserve genetic diversity of this species.

  7. Microsatellite and major histocompatibility complex variation in an endangered rattlesnake, the Eastern Massasauga (Sistrurus catenatus).

    Science.gov (United States)

    Jaeger, Collin P; Duvall, Melvin R; Swanson, Bradley J; Phillips, Christopher A; Dreslik, Michael J; Baker, Sarah J; King, Richard B

    2016-06-01

    Genetic diversity is fundamental to maintaining the long-term viability of populations, yet reduced genetic variation is often associated with small, isolated populations. To examine the relationship between demography and genetic variation, variation at hypervariable loci (e.g., microsatellite DNA loci) is often measured. However, these loci are selectively neutral (or near neutral) and may not accurately reflect genomewide variation. Variation at functional trait loci, such as the major histocompatibility complex (MHC), can provide a better assessment of adaptive genetic variation in fragmented populations. We compared patterns of microsatellite and MHC variation across three Eastern Massasauga (Sistrurus catenatus) populations representing a gradient of demographic histories to assess the relative roles of natural selection and genetic drift. Using 454 deep amplicon sequencing, we identified 24 putatively functional MHC IIB exon 2 alleles belonging to a minimum of six loci. Analysis of synonymous and nonsynonymous substitution rates provided evidence of historical positive selection at the nucleotide level, and Tajima's D provided support for balancing selection in each population. As predicted, estimates of microsatellite allelic richness, observed, heterozygosity, and expected heterozygosity varied among populations in a pattern qualitatively consistent with demographic history and abundance. While MHC allelic richness at the population and individual levels revealed similar trends, MHC nucleotide diversity was unexpectedly high in the smallest population. Overall, these results suggest that genetic variation in the Eastern Massasauga populations in Illinois has been shaped by multiple evolutionary mechanisms. Thus, conservation efforts should consider both neutral and functional genetic variation when managing captive and wild Eastern Massasauga populations.

  8. Analysis of microsatellite instability in CRISPR/Cas9 editing mice.

    Science.gov (United States)

    Huo, Xueyun; Du, Yating; Lu, Jing; Guo, Meng; Li, Zhenkun; Zhang, Shuangyue; Li, Xiaohong; Chen, Zhenwen; Du, Xiaoyan

    2017-03-01

    Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR- associated (Cas) protein 9 system is a novel and powerful tool which is widely used for genome editing. CRISPR/Cas9 is RNA-guided and can lead to desired genomic modifications. However, whether the CRISPR/Cas9-mediated genome editing causes genomic alterations and genomic instability, such as microsatellite instability (MSI), is still unknown. Here we detected MSI in 21 CRISPR/Cas9 mouse strains using a panel of 42 microsatellite loci which were selected from our previous studies. Surprisingly, MSI occurrence was common in CRISPR/Cas9 modified genome, and most of the strains (19/21, 90.5%) examined showed MSI. Of 42 loci examined, 8 loci (8/42, 19.05%) exhibited MSI in the Cas9 editing mice. The Ttll9 (4/42, 9.5%) were the most unstable strains, and D10Mit3 and D10Mit198 (9/21, 42.9%) were considered to be the most "hot" loci in the Cas9 strains we tested. Through analyzing the mutation of microsatellite loci, we provide new insights into the genomic alterations of CRISPR/Cas9 models and it will help us for a better understanding of this powerful technology. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Microsatellite-centromere mapping in Japanese scallop ( Patinopecten yessoensis) through half-tetrad analysis in gynogenetic diploid families

    Science.gov (United States)

    Li, Qi; Qi, Mingjun; Nie, Hongtao; Kong, Lingfeng; Yu, Hong

    2016-06-01

    Gene-centromere mapping is an essential prerequisite for understanding the composition and structure of genomes. Half-tetrad analysis is a powerful tool for mapping genes and understanding chromosomal behavior during meiosis. The Japanese scallop ( Patinopecten yessoensis), a cold-tolerant species inhabiting the northwestern Pacific coast, is a commercially important marine bivalve in Asian countries. In this study, inheritance of 32 informative microsatellite loci was examined in 70-h D-shaped larvae of three induced meiogynogenetic diploid families of P. yessoensis for centromere mapping using half-tetrad analysis. The ratio of gynogenetic diploids was proven to be 100%, 100% and 96% in the three families, respectively. Inheritance analysis in the control crosses showed that 51 of the 53 genotypic ratios observed were in accordance with Mendelian expectations at the 5% level after Bonferroni correction. Seven of the 32 microsatellite loci showed the existence of null alleles in control crosses. The second division segregation frequency ( y) of the microsatellite loci ranged from 0.07 to 0.85 with a mean of 0.38, suggesting the existence of positive interference after a single chiasma formation in some chromosomes in the scallop. Microsatellite-centromere distances ranged from 4 cM to 42 cM under the assumption of complete interference. Information on the positions of centromeres in relation to the microsatellite loci will represent a contribution towards the assembly of genetic maps in the commercially important scallop species.

  10. Genetic diversity analysis in the section Caulorrhizae (genus Arachis) using microsatellite markers

    Science.gov (United States)

    2010-01-01

    Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections. PMID:21637613

  11. Isolation of Microsatellite Markers in a Chaparral Species Endemic to Southern California, Ceanothus megacarpus (Rhamnaceae

    Directory of Open Access Journals (Sweden)

    Caitlin D. A. Ishibashi

    2013-05-01

    Full Text Available Premise of the study: Microsatellite (simple sequence repeat [SSR] markers were developed for Ceanothus megacarpus, a chaparral species endemic to coastal southern California, to investigate potential processes (e.g., fragmentation, genetic drift, and interspecific hybridization responsible for the genetic structure within and among populations distributed throughout mainland and island populations. Methods and Results: Four SSR-enriched libraries were used to develop and optimize 10 primer sets of microsatellite loci containing either di-, tri-, or tetranucleotide repeats. Levels of variation at these loci were assessed for two populations of C. megacarpus. Observed heterozygosity ranged from 0.250 to 0.885, and number of alleles ranged between four and 21 per locus. Eight to nine loci also successfully amplified in three other species of Ceanothus. Conclusions: These markers should prove useful for evaluating the influence of recent and historical processes on genetic variation in C. megacarpus and related species.

  12. Development and characterization of microsatellite markers for the Chinese endangered medicinal plant Tetrastigma hemsleyanum.

    Science.gov (United States)

    Wang, Y H; Chen, N; Zhang, Y C; Fu, C X

    2014-10-31

    Tetrastigma hemsleyanum (Vitaceae) is an endangered medicinal plant endemic to China. Because of its widely known efficacy for treating many health problems, wild resources of this species are currently undergoing a rapid decline. Few studies have been conducted examining the population genetics or development of microsatellite loci for this plant. In this study, 14 microsatellite loci were isolated and characterized for T. hemsleyanum using a double-suppression PCR method. Polymorphisms were tested with a total of 50 individuals from 2 natural populations. The number of alleles per locus ranged from 3-9, with an average of 7 alleles per locus. The observed and expected heterozygosity per locus ranged from 0-1 and from 0.068-0.803, respectively. The polymorphism information content value varied from 0.215-0.760. These loci may facilitate further genetic studies of populations of T. hemsleyanum and provide guidance for their conservation.

  13. Microsatellite markers for genetic studies of the fall armyworm, Spodoptera frugiperda.

    Science.gov (United States)

    Pavinato, V A C; Martinelli, S; de Lima, P F; Zucchi, M I; Omoto, C

    2013-02-08

    We developed six microsatellite markers for the fall armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae). The SSR loci were isolated with enriched genomic library protocol by using native individuals as a genome source for markers. These loci were characterized in 48 individuals and they were tested for the ability to identify candidate migrants exchanged among the samples. The number of alleles per locus ranged from 5 to 18 (10.8 on average). The observed polymorphism information content ranged from 0.172 to 0.891. Beside the lower efficiency to obtain SSR loci, the six microsatellites were polymorphic and sufficiently discriminant for the genetic studies of S. frugiperda; it allowed us to identify migrants with both NJ clustering and the Bayesian methods. These markers will be useful for molecular ecology studies of this highly polyphagous species in order to understand the processes that determine genetic differentiation in the complex agro-ecosystems that it infests and improve local integrated pest management practices.

  14. Development and characterization of 27 microsatellite markers for the mangrove fern, Acrostichum aureum (Pteridaceae)1

    Science.gov (United States)

    Yamamoto, Takashi; Tsuda, Yoshiaki; Mori, Gustavo Maruyama; Cruz, Mariana Vargas; Shinmura, Yoshimi; Wee, Alison K. S.; Takayama, Koji; Asakawa, Takeshi; Yamakawa, Takeru; Suleiman, Monica; Núñez-Farfán, Juan; Webb, Edward L.; Watano, Yasuyuki; Kajita, Tadashi

    2016-01-01

    Premise of the study: Twenty-seven nuclear microsatellite markers were developed for the mangrove fern, Acrostichum aureum (Pteridaceae), to investigate the genetic structure and demographic history of the only pantropical mangrove plant. Methods and Results: Fifty-six A. aureum individuals from three populations were sampled and genotyped to characterize the 27 loci. The number of alleles and expected heterozygosity ranged from one to 15 and 0.000 to 0.893, respectively. Across the 26 polymorphic loci, the Malaysian population showed much higher levels of polymorphism compared to the other two populations in Guam and Brazil. Cross-amplification tests in the other two species from the genus determined that seven and six loci were amplifiable in A. danaeifolium and A. speciosum, respectively. Conclusions: The 26 polymorphic microsatellite markers will be useful for future studies investigating the genetic structure and demographic history of of A. aureum, which has the widest distributional range of all mangrove plants. PMID:27672519

  15. Development of 35 novel microsatellite markers for the two-band anemonefish Amphiprion bicinctus

    KAUST Repository

    Nanninga, Gerrit B.

    2012-12-18

    To investigate population genetic patterns of the anemonefish Amphiprion bicinctus in the Red Sea, we isolated and characterized 35 microsatellite loci using 454-sequencing. Microsatellite sequences were identified using the Tandem Repeats Finder program. The 35 loci were tested on 80 individuals sampled from two spatially separated populations along the Saudi Arabian Red Sea coast. We found a mean of 10. 9 alleles per locus and observed levels of heterozygosity ranged from 0. 4 to 0. 98. All loci were polymorphic, none deviated significantly from Hardy-Weinberg equilibrium, no linkage disequilibrium was observed and there was no evidence for -alleles in both populations. The markers reported here constitute the first specific set for this species, and they are expected to contribute to future studies of connectivity in the Red Sea region. © 2012 Springer Science+Business Media Dordrecht.

  16. Genetic diversity analysis in the section Caulorrhizae (genus Arachis using microsatellite markers

    Directory of Open Access Journals (Sweden)

    Darío A. Palmieri

    2010-01-01

    Full Text Available Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections.

  17. Phylogenetic and Microsatellite Markers for Tulasnella (Tulasnellaceae Mycorrhizal Fungi Associated with Australian Orchids

    Directory of Open Access Journals (Sweden)

    Monica P. Ruibal

    2013-03-01

    Full Text Available Premise of the study: Phylogenetic and microsatellite markers were developed for Tulasnella mycorrhizal fungi to investigate fungal species identity and diversity. These markers will be useful in future studies investigating the phylogenetic relationship of the fungal symbionts, specificity of orchid–mycorrhizal associations, and the role of mycorrhizae in orchid speciation within several orchid genera. Methods and Results: We generated partial genome sequences of two Tulasnella symbionts originating from Chiloglottis and Drakaea orchid species with 454 genome sequencing. Cross-genus transferability across mycorrhizal symbionts associated with multiple genera of Australian orchids (Arthrochilus, Chiloglottis, Drakaea, and Paracaleana was found for seven phylogenetic loci. Five loci showed cross-transferability to Tulasnella from other orchid genera, and two to Sebacina. Furthermore, 11 polymorphic microsatellite loci were developed for Tulasnella from Chiloglottis. Conclusions: Highly informative markers were obtained, allowing investigation of mycorrhizal diversity of Tulasnellaceae associated with a wide variety of terrestrial orchids in Australia and potentially worldwide.

  18. Development of Polymorphic Microsatellite Markers for Indian Tobacco, Lobelia inflata (Campanulaceae

    Directory of Open Access Journals (Sweden)

    P. William Hughes

    2014-04-01

    Full Text Available Premise of the study: Nuclear microsatellite markers were developed for Lobelia inflata (Campanulaceae, an obligately self-fertilizing plant species, for use in the study of temporal fluctuation in allele frequency and of the genetic structure within and among populations. Methods and Results: We developed 28 primer pairs for L. inflata, all of which amplify CT dinucleotide repeats. We evaluated amplification of these loci in 53 L. inflata individuals at three sites in eastern North America and found that 24 loci showed microsatellite polymorphism. We also found that 16 loci amplified successfully in L. cardinalis, and 11 amplified successfully in L. siphilitica. Conclusions: These primers will be useful for assessing allelic diversity within and among populations of L. inflata, and show potential for use in congeneric species.

  19. Development of microsatellite markers for Viscum coloratum (Santalaceae) and their application to wild populations1

    Science.gov (United States)

    Kim, Bo-Yun; Park, Han-Sol; Kim, Soonok; Kim, Young-Dong

    2017-01-01

    Premise of the study: Microsatellite primers were developed for Viscum coloratum (Santalaceae), a semiparasitic medicinal plant that is known for its anticancer properties. Due to excessive human harvesting and loss of suitable habitat of its populations, it has become a potentially threatened species requiring immediate conservation efforts. Methods and Results: Based on transcriptome data for V. coloratum, 124 primer pairs were randomly selected for initial validation, of which 19 yielded polymorphic microsatellite loci, with two to six alleles per locus. The usefulness of these markers was assessed for 60 individuals representing three populations of V. coloratum. Observed and expected heterozygosity values ranged from 0.033 to 0.833 and 0.032 to 0.672, respectively. Cross-species amplification for 19 loci in the related species V. album was conducted. Conclusions: The 19 newly developed loci are expected to be useful for studying the population genetics and ecological conservation of V. coloratum. PMID:28090408

  20. Development of Microsatellite Markers in the Deep-Sea Cup Coral Desmophyllum dianthus by 454 Sequencing and Cross-Species Amplifications in Scleractinia Order.

    Science.gov (United States)

    Addamo, Anna M; García-Jiménez, Ricardo; Taviani, Marco; Machordom, Annie

    2015-01-01

    Microsatellite loci were isolated for the first time for the deep-sea coral Desmophyllum dianthus, using 454 GS-FLX Titanium pyrosequencing. We developed conditions for amplifying 24 markers in 10 multiplex reactions. Three to 16 alleles per locus were detected across 25 samples analyzed from Santa Maria di Leuca coral province (Mediterranean Sea). For the 24 polymorphic loci, observed and expected heterozygosities ranged from 0.211 to 0.880 and 0.383 to 0.910, respectively; 3 loci deviated from Hardy-Weinberg equilibrium, after null allele and sequential Holm-Bonferroni corrections. These newly isolated microsatellites are very useful genetic markers that provide data for future conservation strategies. Cross-amplification of these microsatellites, tested in 46 coral species, representing 40 genera, and 10 families of the phylum Cnidaria, produced informative allelic profiles for 1 to 24 loci. The utility of extending analyses to cross-species amplifications is also discussed.

  1. Microsatellite analyses of the trout of northwest Mexico

    Science.gov (United States)

    Nielsen, J.L.; Sage, G.K.

    2001-01-01

    The trout of northwest Mexico represent an undescribed group of fish considered part of the Oncorhynchus mykiss (Pacific trout) complex of species and subspecies. Recent genetic studies have shown these fish to have important genetic diversity and a unique evolutionary history when compared to coastal rainbow trout. Increased levels of allelic diversity have been found in this species at the southern extent of its range. In this study we describe the trout in the Sierra Madre Occidental from the rios Yaqui, Mayo, Casas Grandes and de Bavispe, and their relationship to the more southern distribution of Mexican golden trout (O. chrysogaster) using 11 microsatellite loci. Microsatellite allelic diversity in Mexican trout was high with a mean of 6.6 alleles/locus, average heterozygosity = 0.35, and a mean Fst = 0.43 for all loci combined. Microsatellite data were congruent with previously published mtDNA results showing unique panmictic population structure in the Rio Yaqui trout that differs from Pacific coastal trout and Mexican golden trout. These data also add support for the theory of headwaters transfer of trout across the Continental Divide from tributaries of the Rio de Bavispe into the Rio Casas Grandes. Rio Mayo trout share a close genetic relationship to trout in Rio Yaqui, but sample sizes from the Rio Mayo prevent significant comparisons in this study. Microsatellite analyses show significant allelic frequency differences between Rio Yaqui trout and O. chrysogaster in Sinaloa and Durango Mexico, adding further support for a unique evolutionary status for this group of northwestern Mexican trout.

  2. Evolutionary process of a tetranucleotide microsatellite locus in Acipenseriformes

    Indian Academy of Sciences (India)

    Zhao Jun Shao; Eric Rivals; Na Zhao; Sovan Lek; Jianbo Chang; Patrick Berrebi

    2011-08-01

    The evolutionary dynamics of the tetra-nucleotide microsatellite locus Spl-106 were investigated at the repeat and flanking sequences in 137 individuals of 15 Acipenseriform species, giving 93 homologous sequences, which were detected in 11 out of 15 species. Twenty-three haplotypes of flanking sequences and three distinct types of repeats, type I, type II and type III, were found within these 93 sequences. The MS-Align phylogenetic method, newly applied to microsatellite sequences, permitted us to understand the repeat and flanking sequence evolution of Spl-106 locus. The flanking region of locus Spl-106 was highly conserved among the species of genera Acipenser, Huso and Scaphirhynchus, which diverged about 150 million years ago (Mya). The rate of flanking sequence divergence at the microsatellite locus Spl-106 in sturgeons is between 0.011% and 0.079% with an average at 0.028% per million years. Sequence alignment and phylogenetic trees produced by MS-Align showed that both the flanking and repeat regions can cluster the alleles of different species into Pacific and Atlantic lineages. Our results show a synchronous evolutionary pattern between the flanking and repeat regions. Moreover, the coexistence of different repeat types in the same species, even in the same individual, is probably due to two duplication events encompassing the locus Spl-106 that occurred during the divergence of Pacific lineage. The first occured before the diversification of Pacific species (121–96 Mya) and led to repeat types I and II. The second occurred more recently, just before the speciation of A. sinensis and A. dabryanus (69–10 Mya), and led to repeat type III. Sequences in the same species with different repeat types probably corresponds to paralogous loci. This study sheds a new light on the evolutionary mechanisms that shape the complex microsatellite loci involving different repeat types.

  3. Microsatellites reveal high genetic diversity within colonies of Camponotus ants.

    Science.gov (United States)

    Gertsch, P; Pamilo, P; Varvio, S L

    1995-04-01

    In order to characterize the sociogenetic structure of colonies in the carpenter ants Camponotus herculeanus and C. ligniperda, we have developed microsatellite markers. The three loci studied were either fixed for different alleles in the two species or showed different patterns of polymorphisms. Genotyping of workers and males showed that the broods of C. ligniperda include several matrilines, a rare phenomenon in the genus. Five alleles from a locus polymorphic in both species were sequenced from the respective PCR-products. A part of the length variation appeared to be due to changes outside the repeat sequence, and some PCR products of an equal length had a different number of dinucleotide repeats.

  4. Isolation, characterization, and multiplexing of novel microsatellite markers for the tropical scalloped spiny lobster (Panulirus homarus).

    Science.gov (United States)

    Delghandi, M; Goddard, S; Jerry, D R; Dao, H T; Afzal, H; Al-Jardani, S S

    2015-12-29

    Of the various spiny lobster species in the tropical and subtropical Indo-West Pacific region, the tropical scalloped spiny lobster (Panulirus homarus) supports one of the most commercially valuable fishery resources in many coastal African and Asian countries. The last decade has witnessed a serious decline in the wild populations of this species. Knowledge of the genetic basis of spiny lobster population structure is a prerequisite to achieve a sustainable fisheries management for this species. Here, we describe 13 novel polymorphic microsatellite markers developed for P. homarus, using a cross-species primer design strategy based on P. ornatus Roche 454 shot-gun generated sequencing. Microsatellite polymorphisms were assessed in 96 unrelated P. homarus individuals of a natural population, with the number of alleles per locus varying from 2 to 14, the observed and expected heterozygosity from 0.00 to 0.78 and from 0.03 to 0.79, respectively, and with only four loci (Pho-G27, Pho-G32, Pho-G36, and Pho-G58) deviating from Hardy- Weinberg equilibrium. Genetic linkage disequilibrium analysis between all pairs of the loci showed significant departure from the null hypothesis between loci Pho-G22 - Pho-G30, and Pho-G30 - Pho-G35. The successful cross amplification of these microsatellites highlights the potential of the developed microsatellites for future population genetic research within the different Panulirus species.

  5. 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.

  6. Development of microsatellite markers and detection of genetic variation between Goniozus wasp populations.

    Science.gov (United States)

    Khidr, Sahand K; Hardy, Ian C W; Zaviezo, Tania; Mayes, Sean

    2014-03-20

    Molecular genetic markers reveal differences between genotypes according to the presence of alleles (the same or different) at target loci. Microsatellite markers are especially useful co-dominant markers that have been used in a wide range of studies to elucidate the population structure and dynamics of a range of organisms, including agriculturally beneficial insects such as parasitic wasps (parasitoids). In the present study, twelve primer pairs were designed for the south Asian , Goniozus nephantidis (Muesebeck) (Hymenoptera: Bethylidae), and 24 for its New World congener, Goniozus legneri Gordh, parasitoids of the larvae of the lepidopteran coconut pest Opisina arenosella Walker (Lepidoptera: Crytophasidae) and other lepidopteran pests, respectively, in order to investigate polymorphism within and between populations. The wasps fingerprinted were a total of 85 G. nephantidis and G. legneri, including individuals belonging to three putatively different strains of G. legneri. Annealing gradient tests (50-65°C) were conducted to study the quality of the PCR amplification across an annealing temperature gradient using a mixed genotype DNA template from each species separately. Seven primer pairs, which amplified clear products of approximately the expected size of G. nephantidis and 18 of G. legneri, were then selected for capillary analysis for fragment size determination on a Beckmann CEQ 8000. Neither G. nephantidis nor G. legneri were polymorphic within populations. However, there were six primer pairs that did show polymorphism between G. legneri populations that originated from different geographical areas within South America (Uruguay and Chile). Furthermore, one primer pair revealed diversity between the two strains collected within Chile. One of the markers was subsequently used to provide unbiased assessment of primary sex ratio in G. legneri.

  7. Morphological and microsatellite diversity associated with ecological factors in natural populations of Medicago laciniata Mill. (Fabaceae)

    Indian Academy of Sciences (India)

    Mounawer Badri; Adel Zitoun; Houcine Ilahi; Thierry Huguet; Mohamed Elarbi Aouani

    2008-12-01

    Genetic variability in 10 natural Tunisian populations of Medicago laciniata were analysed using 19 quantitative traits and 12 polymorphic microsatellite loci. A large degree of genetic variability within-populations and among-populations was detected for both quantitative characters and molecular markers. High genetic differentiation among populations for quantitative traits was seen, with $Q_{ST} = 0.47$, and $F_{ST} = 0.47$ for microsatellite markers. Several quantitative traits displayed no statistical difference in the levels of $Q_{ST}$ and $F_{ST}$. Further, significant correlations between quantitative traits and eco-geographical factors suggest that divergence in the traits among populations may track environmental differences. There was no significant correlation between genetic variability at quantitative traits and microsatellite markers within populations. The site-of-origin of eco-geographical factors explain between 18.13% and 23.40% of genetic variance among populations at quantitative traits and microsatellite markers, respectively. The environmental factors that most influence variation in measured traits among populations are assimilated phosphorus (P205) and mean annual rainfall, followed by climate and soil texture, altitude and organic matter. Significant associations between eco-geographical factors and gene diversity, $H_{e}$, were established in five-microsatellite loci suggesting that these simple sequence repeats (SSRs) are not necessarily biologically neutral.

  8. Molecular Analysis of Microsatellite Mutagenesis in Soybean (Glycine max)%大豆微卫星诱发突变的分子分析

    Institute of Scientific and Technical Information of China (English)

    朱保葛; 孙勇如

    2004-01-01

    Microsatellite or SSR marker is an efficient tool for plant genotype identification, molecular mapping and marker-assisted selection. Objective of this study is to analyze the mutagenized microsatellite variations in soybean genome and reveal nature of these mutations. In the present study, mutations at fifteen microsatellite loci were detected in genomic DNAs of soybean mutant E182 induced by EMS (ethyne metyl sulfate) using PCR amplification of 485 pairs of SSR primers. These fifteen mutagenized microsatellite loci with repeat number variation were Satt005, Satt117, Satt185, Satt282, Satt290, Satt420, Satt452, Satt483, Satt569, Satt579, Satt600, Satt602, Sat_086, Sat_107 and Sat_135, respectively. Sequencing results of these fifteen loci indicated that microsatellite sequences at Satt282, Satt483, Satt579, Satt600 and Satt602 loci were respectively deleted 1-, 3-, 8-, 20- and 1-trinucleotide (all [ATT]1-20 except for [CAA]8[TAA]12 at Satt600 locus) repeats, which made allele sizes at these five loci decrease 3, 9, 24, 60 and 3 bp, respectively. And while microsatellite sequences at the other ten mutated loci, Satt005, Satt117, Satt185, Satt290, Satt420, Satt452, Satt569 and Sat_086, Sat_107, Sat_135, were respectively inserted 1-, 6-, 6-, 3-, 4-, 3-, 8-trinucleotide repeats (ATT)1-8 and 12-, 6-, 16-dinucleotide repeats (AT)6-16, making allele sizes at these ten loci increase 3, 18, 18, 9, 12, 9, 24, 24, 12, 32 bp, respectively. On the other hand, eleven events of base mutations were detected in flanking regions at seven (Sat-107, Satt185, Satt282, Satt420, Satt569, Satt579 and Satt600) of fifteen mutated microsatellite loci. These base mutations consisted of 6 transitions (4T→C and 2 A→G), 2 transvertions (A→T and T→A), 1 insertion (T) and 2 deletions (A and T). The experimental results proved that EMS mutagenesis could cause different types of mutations at microsatellite multilocus in soybean genome, including repeat number variations in microsatellite

  9. Informativeness of minisatellite and microsatellite markers for genetic analysis in papaya.

    Science.gov (United States)

    Oliveira, G A F; Dantas, J L L; Oliveira, E J

    2015-10-01

    The objective of this study was to evaluate information on minisatellite and microsatellite markers in papaya (Carica papaya L.). Forty minisatellites and 91 microsatellites were used for genotyping 24 papaya accessions. Estimates of genetic diversity, genetic linkage and analyses of population structure were compared. A lower average number of alleles per locus was observed in minisatellites (3.10) compared with microsatellites (3.57), although the minisatellites showed rarer alleles (18.54 %) compared with microsatellite (13.85 %). Greater expected (He = 0.52) and observed (Ho = 0.16) heterozygosity was observed in the microsatellites compared with minisatellites (He = 0.42 and Ho = 0.11), possibly due to the high number of hermaphroditic accessions, resulting in high rates of self-fertilization. The polymorphic information content and Shannon-Wiener diversity were also higher for microsatellites (from 0.47 to 1.10, respectively) compared with minisatellite (0.38 and 0.85, respectively). The probability of paternity exclusion was high for both markers (>0.999), and the combined probability of identity was from 1.65(-13) to 4.33(-38) for mini- and micro-satellites, respectively, which indicates that both types of markers are ideal for genetic analysis. The Bayesian analysis indicated the formation of two groups (K = 2) for both markers, although the minisatellites indicated a substructure (K = 4). A greater number of accessions with a low probability of assignment to specific groups were observed for microsatellites. Collectively, the results indicated higher informativeness of microsatellites. However, the lower informative power of minisatellites may be offset by the use of larger number of loci. Furthermore, minisatellites are subject to less error in genotyping because there is greater power to detect genotyping systems when larger motifs are used.

  10. Whole genome scan to detect quantitative trait loci for conformation and functional traits in dairy cattle

    NARCIS (Netherlands)

    Schrooten, C.; Bovenhuis, H.; Coppieters, W.; Arendonk, van J.A.M.

    2000-01-01

    A granddaughter design was used to locate quantitative trait loci determining conformation and functional traits in dairy cattle. In this granddaughter design, consisting of 20 Holstein Friesian grandsires and 833 sons, genotypes were determined for 277 microsatellite markers covering the whole geno

  11. Microsatellite markers for Dayaoshania cotinifolia (Gesneriaceae), a critically endangered perennial herb.

    Science.gov (United States)

    Zhang, Bing; Wang, Hong-Wei; Cheng, Yue-Qin; Ye, Yong-Zhong; Wang, Zhao-Shan

    2011-09-01

    Microsatellite primers were developed for the critically endangered species Dayaoshania cotinifolia (Gesneriaceae) to evaluate population genetic diversity and detect population history. • In our study, 15 primer sets were developed using an enriched genomic library. These are the first microsatellite loci developed for this genus. Genetic diversity was measured using 40 individuals. The number of alleles per locus ranged from one to six, and the incidence of observed heterozygosities was 0.365 and 0.410 in two populations. • The described markers will be useful in future population genetics studies of this critically endangered species.

  12. Nine novel, polymorphic microsatellite markers for the study of threatened Caribbean acroporid corals.

    Science.gov (United States)

    Baums, I B; Devlin-Durante, M K; Brown, L; Pinzón, J H

    2009-07-01

    Caribbean reef-building corals in the genus Acropora have been declining dramatically since the 1980s and are now listed as threatened. The study of their complex reproductive system (mixed asexual and sexual) and their population structure requires highly polymorphic nuclear genetic markers. Of eight previously developed microsatellite loci for A. palmata, only five behaved in a Mendelian fashion and only four reliably amplified the sister species, A. cervicornis. Here, nine novel microsatellite markers are presented that dramatically increase the power to distinguish between asexual and sexual reproductive events and may help to refine population boundaries and gene flow across their ranges.

  13. Typing dinucleotide repeat loci using microplate array diagonal gel electrophoresis: proof of principle.

    Science.gov (United States)

    Rodríguez, Santiago; Chen, Xiao-He; Day, Ian N M

    2004-04-01

    Polymorphic dinucleotide repeat loci ('microsatellite markers') are found in varying abundance throughout the genomes of most organisms. They have been extensively used for genetic studies, but conventional techniques used for their genotyping require sophisticated equipment. Microplate array diagonal gel electrophoresis (MADGE) has previously been extended to economical high-throughput genotyping of trinucleotide and tetranucleotide microsatellite amplicons. However, the capability of this technique to resolve the alleles of dinucleotide repeat loci has not been explored previously. Here we show that a modified microsatellite-MADGE approach can provide sufficient resolution for dinucleotide repeat typing. This enables economical and convenient set up for analysis of single markers in many samples in parallel, suitable, for example, for population association studies.

  14. Novel polymorphic microsatellite markers developed for a common reef sponge, Stylissa carteri

    KAUST Repository

    Giles, E.C.

    2013-04-04

    Despite the ubiquitous role sponges play in reef ecosystem dynamics, little is known about population-level connectivity in these organisms. The general field of population genetics in sponges remains in its infancy. To date, microsatellite markers have only been developed for few sponge species and no sponge population genetics studies using microsatellites have been conducted in the Red Sea. Here, with the use of next-generation sequencing, we characterize 12 novel polymorphic loci for the common reef sponge, Stylissa carteri. The number of alleles per loci ranged between three and eight. Observed heterozygosity frequencies (Ho) ranged from 0.125 to 0.870, whereas expected (He) heterozygosity frequencies ranged from 0.119 to 0.812. Only one locus showed consistent deviations from Hardy-Weinberg equilibrium (HWE) in both populations and two loci consistently showed the possible presence of null alleles. No significant linkage disequilibrium was detected for any pairs of loci. These microsatellites will be of use for numerous ecological studies focused on this common and abundant sponge. 2013 The Author(s).

  15. Genetic variation of Garra rufa fish in Kermanshah and Bushehr provinces, Iran, using SSR microsatellite markers

    Directory of Open Access Journals (Sweden)

    Ali Shabani

    2013-09-01

    Full Text Available Six highly variable microsatellite loci were used to investigate the genetic diversity and population structure of the Garra rufa in Kermanshah and Bushehr provinces, Iran. All of the 6 microsatellite loci screened in this study showed polymorphism. A total of 90 individual fish from 3 populations were genotyped and 60 alleles were observed in all loci. The number of alleles per locus ranged from 6 to14. The average allelic number of these polymorphic markers was 10. The averages of observed (Ho and expected heterozygosity (He was 0.529 and 0.826, respectively. The genetic distance values ranged between 0.235-0.570. The UPGMA dendrogram based on genetic distance resulted in three clusters: Gamasiab population alone was classified as one and the other two populations as the second cluster. This study revealed a fairly high level of genetic variation in the microsatellite loci within the three populations, and identified distinct population groups of Garra rufa. This study gains significance for the analysis of the populations’ genetic diversity as well as the management of this important fish resource.

  16. Evaluation of Parentage Test in some of Holstein Cattle Using Fluorescent Labeled Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    M. Hashemi

    2012-09-01

    Full Text Available In order to evaluate paternity test using microsatellite markers, a small sample of Iranian Holstein cattle population including 8 unknown individuals without any given prior knowledge on their genetic relationships were tested using 12 microsatellite loci recommended by International Society of Animal Genetics (ISAG. They were genotyped by a multiplex PCR set consisted all 12 fluorescently labeled primer pairs. Allele and genotype frequencies were estimated and simulated by CERVUS 2.0 software for paternity analysis. Using this software parentage test and relationship between samples have been determined and confirmed by sample’s provider. Paternity relationship including one or two parents for an offspring and also repeated samples were observed. The average expected heterozygosity of 11 analyzed loci and the mean value for PIC was 0.72 and 0.631 respectively. Except TGLA53 locus that was excluded from further analyses due to low quality of alleles and genotype detection, total exclusion probability of 11 loci showed that the paternity test using microsatellite loci mentioned here can be successfully implicated in large scale in Holstein dairy cattle population in Iran.

  17. Development of Microsatellites for Population Genetic Analyses of the Granulate Ambrosia Beetle (Coleoptera: Curculionidae).

    Science.gov (United States)

    Husseneder, Claudia; Park, Jong-Seok; Werle, Christopher T; Adamczyk, John J

    2017-06-01

    Limited male dispersal and local mating in ambrosia beetles are expected to result in extreme inbreeding and highly structured populations. In this study, we developed microsatellite markers for the granulate ambrosia beetle, Xylosandrus crassiusculus (Motschulsky), for use in future studies into population and family structure of this invasive pest species. We employed de novo next-generation sequencing to generate whole genome shotgun sequences for the characterization of microsatellite loci. Approximately 6% of the 84,024 contigs generated from Hi-Seq Illumina 2x250bp sequencing contained microsatellites with at least four repeats of di-, tri-, tetra-, penta-, and hexamers. Primers were synthesized for 40 microsatellite loci with trimer repeat units. Twenty-four primer pairs yielded consistent PCR products of unique loci and were validated for population genetic application using three sample groups each containing 20 X. crassiusculus individuals from Mississippi. Thirteen loci were found to be polymorphic with up to five alleles per population. The two beetle sample groups from Pearl River County (Poplarville and McNeill) belonged genetically to the same population. The population from Lamar County (Purvis) was genetically distinct, separated by a moderate genetic distance (FST = 0.11) and five unique alleles (with >5% frequency). Consistent with the perceived mating structure (incest of females with flightless males), the populations showed homozygote excess at most loci, as indicated by the coefficients of inbreeding (FIT = 0.45 and FIS = 0.37) and high mean relatedness among individuals (r = 0.15). © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  18. A rapid and cost-effective approach for the development of polymorphic microsatellites in non-model species using paired-end RAD sequencing.

    Science.gov (United States)

    Xue, Dong-Xiu; Li, Yu-Long; Liu, Jin-Xian

    2017-06-20

    As one of the most informative and versatile DNA-based markers, microsatellites have been widely used in population and conservation genetic studies. However, the development of microsatellites has traditionally been laborious, time-consuming, and expensive. In the present study, a rapid and cost-effective "RAD-seq-Assembly-Microsatellite" approach was developed to identify abundant microsatellite markers in non-model species using the roughskin sculpin Trachidermus fasciatus as a representative. Overlapping paired-end Illumina reads generated by restriction-site-associated DNA sequencing (RAD-seq) were clustered based on the similarity of reads containing the restriction enzyme recognition site and then assembled into contigs, which were used for microsatellite discovery and primer design. A total of 121,750 RAD contigs were generated with a mean length of 522 bp, and 19,782 contigs contained microsatellite motifs. A total of 156,150 primer pairs were successfully designed based on 16,497 contigs containing priming sites. Experimental validation of 52 randomly selected microsatellite loci demonstrated that 45 (86.54%) loci were successfully amplified and polymorphic in two geographically isolated populations of T. fasciatus. Compared with traditional approaches based on DNA cloning and other approaches based on next-generation sequencing, our newly developed approach could yield thousands of microsatellite loci with much higher successful amplification rate and lower costs, especially for non-model species with shallow background of genomic information. The "RAD-seq-Assembly-Microsatellite" approach holds great promise for microsatellite development in future ecological and evolutionary studies of non-model species.

  19. Development of an integrative database with 499 novel microsatellite markers for Macaca fascicularis

    Directory of Open Access Journals (Sweden)

    Higashino Atsunori

    2009-06-01

    Full Text Available Abstract Background Cynomolgus macaques (Macaca fascicularis are a valuable resource for linkage studies of genetic disorders, but their microsatellite markers are not sufficient. In genetic studies, a prerequisite for mapping genes is development of a genome-wide set of microsatellite markers in target organisms. A whole genome sequence and its annotation also facilitate identification of markers for causative mutations. The aim of this study is to establish hundreds of microsatellite markers and to develop an integrative cynomolgus macaque genome database with a variety of datasets including marker and gene information that will be useful for further genetic analyses in this species. Results We investigated the level of polymorphisms in cynomolgus monkeys for 671 microsatellite markers that are covered by our established Bacterial Artificial Chromosome (BAC clones. Four hundred and ninety-nine (74.4% of the markers were found to be polymorphic using standard PCR analysis. The average number of alleles and average expected heterozygosity at these polymorphic loci in ten cynomolgus macaques were 8.20 and 0.75, respectively. Conclusion BAC clones and novel microsatellite markers were assigned to the rhesus genome sequence and linked with our cynomolgus macaque cDNA database (QFbase. Our novel microsatellite marker set and genomic database will be valuable integrative resources in analyzing genetic disorders in cynomolgus macaques.

  20. Comparing geographical genetic differentiation between candidate and noncandidate loci for adaptation strengthens support for parallel ecological divergence in the marine snail Littorina saxatilis.

    Science.gov (United States)

    Galindo, J; Morán, P; Rolán-Alvarez, E

    2009-03-01

    The Galician sympatric ecotypes of Littorina saxatilis have been proposed as a model system for studying parallel ecological speciation. Such a model system makes a clear prediction: candidate loci (for divergent adaptation) should present a higher level of geographical differentiation than noncandidate (neutral) loci. We used 2356 amplified fragment length polymorphisms (AFLPs) and four microsatellite loci to identify candidate loci for ecological adaptation using the F(ST) outlier method. Three per cent of the studied AFLP loci were identified as candidate loci associated with adaptation, after multitest adjustments, thus contributing to ecotype differentiation (candidate loci were not detected within ecotypes). Candidate and noncandidate loci were analysed separately at four different F(ST) partitions: differences between ecotypes (overall and local), differences between localities and micro-geographical differences within ecotypes. The magnitude of F(ST) differed between candidate and noncandidate loci for all partitions except in the case of micro-geographical differentiation within ecotypes, and the microsatellites (putatively neutral) showed an identical pattern to noncandidate loci. Thus, variation in candidate loci is determined partially independent by divergent natural selection (in addition to stochastic forces) at each locality, while noncandidate loci are exclusively driven by stochastic forces. These results support the evolutionary history described for these particular populations, considered to be a clear example of incomplete sympatric ecological speciation.

  1. Novel microsatellite markers for the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae) and effects of null alleles on population genetics analyses.

    Science.gov (United States)

    Song, W; Cao, L-J; Wang, Y-Z; Li, B-Y; Wei, S-J

    2016-11-07

    The oriental fruit moth (OFM) Grapholita molesta (Lepidoptera: Tortricidae) is an important economic pest of stone and pome fruits worldwide. We sequenced the OFM genome using next-generation sequencing and characterized the microsatellite distribution. In total, 56,674 microsatellites were identified, with 11,584 loci suitable for primer design. Twenty-seven polymorphic microsatellites, including 24 loci with trinucleotide repeat and three with pentanucleotide repeat, were validated in 95 individuals from four natural populations. The allele numbers ranged from 4 to 40, with an average value of 13.7 per locus. A high frequency of null alleles was observed in most loci developed for the OFM. Three marker panels, all of the loci, nine loci with the lowest null allele frequencies, and nine loci with the highest null allele frequencies, were established for population genetics analyses. The null allele influenced estimations of genetic diversity parameters but not the OFM's genetic structure. Both a STRUCTURE analysis and a discriminant analysis of principal components, using the three marker panels, divided the four natural populations into three groups. However, more individuals were incorrectly assigned by the STRUCTURE analysis when the marker panel with the highest null allele frequency was used compared with the other two panels. Our study provides empirical research on the effects of null alleles on population genetics analyses. The microsatellites developed will be valuable markers for genetic studies of the OFM.

  2. Microsatellite marker development by multiplex ion torrent PGM sequencing: a case study of the endangered Odorrana narina complex of frogs.

    Science.gov (United States)

    Igawa, Takeshi; Nozawa, Masafumi; Nagaoka, Mai; Komaki, Shohei; Oumi, Shohei; Fujii, Tamotsu; Sumida, Masayuki

    2015-01-01

    The endangered Ryukyu tip-nosed frog Odorrana narina and its related species, Odorrana amamiensis, Odorrana supranarina, and Odorrana utsunomiyaorum, belong to the family Ranidae and are endemically distributed in Okinawa (O. narina), Amami and Tokunoshima (O. amamiensis), and Ishigaki and Iriomote (O. supranarina and O. utsunomiyaorum) Islands. Because of varying distribution patterns, this species complex is an intrinsic model for speciation and adaptation. For effective conservation and molecular ecological studies, further genetic information is needed. For rapid, cost-effective development of several microsatellite markers for these and 2 other species, we used next-generation sequencing technology of Ion Torrent PGM™. Distribution patterns of repeat motifs of microsatellite loci in these modern frog species (Neobatrachia) were similarly skewed. We isolated and characterized 20 new microsatellite loci of O. narina and validated cross-amplification in the three-related species. Seventeen, 16, and 13 loci were cross-amplified in O. amamiensis, O. supranarina, and O. utsunomiyaorum, respectively, reflecting close genetic relationships between them. Mean number of alleles and expected heterozygosity of newly isolated loci varied depending on the size of each inhabited island. Our findings suggested the suitability of Ion Torrent PGM™ for microsatellite marker development. The new markers developed for the O. narina complex will be applicable in conservation genetics and molecular ecological studies.

  3. Present and past microsatellite variation and assessment of genetic structure in Eurasian badger (Meles meles) in Denmark

    NARCIS (Netherlands)

    Pertoldi, C; Loeschcke, [No Value; Randi, E; Madsen, AB; Hansen, MM; Bijlsma, R; Van De Zande, L

    2005-01-01

    During the past 50 years the number of badgers (Meles meles) in Denmark has declined by c. 50%. To assess the genetic consequences of the demographic decline, six DNA-microsatellite loci were used to analyse 139 badger tissue-samples, which were collected in 1995-98 from three zones (1, 2 and 3) in

  4. Genetic characterization of commercial honey bee (Hymenoptera: Apidae) populations in the United States by using mitochondrial and microsatellite markers

    Science.gov (United States)

    D. A. Delaney; M.D. Meixner; N.M. Schiff; W.S. Sheppard

    2009-01-01

    Genetic diversity levels within and between the two commercial breeding areas in theUnited States were analyzed using the DraI restriction fragment length polymorphism of the COICOII mitochondrial region and 10 polymorphic microsatellite loci. The western commercial breeding population (WCBP) and the southeastern commercial...

  5. Multiple paternity and female-biased mutation at a microsatellite locus in the olive ridley sea turtle (Lepidochelys olivacea)

    NARCIS (Netherlands)

    Hoekert, W.E.J.; Neufeglise, N.; Schouten, A.D.; Menken, S.B.J.

    2002-01-01

    Multiple paternity in the olive ridley sea turtle (Lepidochelys olivacea) population nesting in Suriname was demonstrated using two microsatellite loci, viz., Ei8 and Cm84. The large number of offspring sampled per clutch (70 on average, ranging from 15 to 103) and the number of alleles found at the

  6. Polymorphism, monomorphism, and sequences in conserved microsatellites in primate species.

    Science.gov (United States)

    Blanquer-Maumont, A; Crouau-Roy, B

    1995-10-01

    Dimeric short tandem repeats are a source of highly polymorphic markers in the mammalian genome. Genetic variation at these hypervariable loci is extensively used for linkage analysis, for the identification of individuals, and may be useful for interpopulation and interspecies studies. In this paper, we analyze the variability and the sequences of a segment including three microsatellites, first described in man, in several species of primates (chimpanzee, orangutan, gibbon, and macaque) using the heterologous primers (man primers). This region is located on the human chromosome 6p, near the tumor necrosis factor genes, in the major histocompatibility complex. The fact that these primers work in all species studied indicates that they are conserved throughout the different lineages of the two superfamilies, the Hominoidea and the Cercopithecidea, represented by the macaques. However, the intervening sequence displays intraspecific and interspecific variability. The sites of base substitutions and the insertion/deletion events are not evenly distributed within this region. The data suggest that it is necessary to have a minimal number of repeats to increase the rate of mutation sufficiently to allow the development of polymorphism. In some species, the microsatellites present single base variations which reduce the number of contiguous repeats, thus apparently slowing the rate of additional slippage events. Species with such variations or a low number of repeats are monomorphic. These microsatellite sequences are informative in the comparison of closely related species and reflect the phylogeny of the Old World monkeys, apes, and man.

  7. Heterologous microsatellite primer pairs informative for the whole genus Arachis

    Directory of Open Access Journals (Sweden)

    Andrea Akemi Hoshino

    2006-01-01

    Full Text Available The genus Arachis currently comprises 69 described species, some of which have potential and real value as human and animal foods. These Arachis species have been collected and maintained in germplasm banks to provide material that can be used as sources of genes in breeding programs and for the selection of new cultivars. One of the principal objectives of germplasm conservation is the evaluation of genetic variability, which is best conducted using molecular markers. We investigated the use of heterologous primers to amplify microsatellite loci that could be used to evaluate genetic variability in Arachis germplasm. Fifteen microsatellite primer pairs were tested in 76 accessions of 34 species from the nine Arachis sections. The data indicated that heterologous primers were very useful in Arachis since they had high transferability among the species (91% and allowed the amplification of very polymorphic putative loci, which allowed both the characterization of most accessions and to make inferences about the mating systems of some species analyzed. Our data also revealed that the germplasm analyzed showed high variability, even when represented by few accessions.

  8. Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes.

    Directory of Open Access Journals (Sweden)

    Fábio Raposo do Amaral

    Full Text Available Sequence capture of ultraconserved elements (UCEs associated with massively parallel sequencing has become a common source of nuclear data for studies of animal systematics and phylogeography. However, mitochondrial and microsatellite variation are still commonly used in various kinds of molecular studies, and probably will complement genomic data in years to come. Here we show that besides providing abundant genomic data, UCE sequencing is an excellent source of both sequences for microsatellite loci design and complete mitochondrial genomes with high sequencing depth. Identification of dozens of microsatellite loci and assembly of complete mitogenomes is exemplified here using three species of Poospiza warbling finches from southern and southeastern Brazil. This strategy opens exciting opportunities to simultaneously analyze genome-wide nuclear datasets and traditionally used mtDNA and microsatellite markers in non-model amniotes at no additional cost.

  9. Mythematics Solving the Twelve Labors of Hercules

    CERN Document Server

    Huber, Michael

    2009-01-01

    How might Hercules, the most famous of the Greek heroes, have used mathematics to complete his astonishing Twelve Labors? From conquering the Nemean Lion and cleaning out the Augean Stables, to capturing the Erymanthean Boar and entering the Underworld to defeat the three-headed dog Cerberus, Hercules and his legend are the inspiration for this book of fun and original math puzzles. While Hercules relied on superhuman strength to accomplish the Twelve Labors, Mythematics shows how math could have helped during his quest. How does Hercules defeat the Lernean Hydra and stop its heads from multip

  10. Development of novel microsatellite markers for Holothurian scabra (Holothuriidae), Apostichopus japonicas (Stichopodidae) and cross-species testing in other sea cucumbers

    Science.gov (United States)

    Shangguan, Jingbo; Li, Zhongbao

    2017-06-01

    Thirty-five new microsatellite loci from the sea cucumbers Holothurian scabra (Jaeger, 1833) and Apostichopus japonicas (Selenka, 1867) were screened and characterized using the method of magnetic bead enrichment. Of the twenty-four polymorphic loci tested, eighteen were consistent with Hardy-Weinberg equilibrium after a modified false discovery rate (B-Y FDR) correction, whereas six showed statistically significant deviations (CHS2 and CHS11: P universality of all loci were generally low, the results of the cross-species study showed that the markers can be applied to identify individuals to species according to the presence or absence of specific microsatellite alleles. The microsatellite markers reported here will contribute to the study of genetic diversity, assisted breeding, and population conservation in sea cucumbers, as well as allow for the identification of individuals to closely related species.

  11. Microsatellite analysis of medfly bioinfestations in California.

    Science.gov (United States)

    Bonizzoni, M; Zheng, L; Guglielmino, C R; Haymer, D S; Gasperi, G; Gomulski, L M; Malacrida, A R

    2001-10-01

    The Mediterranean fruit fly, Ceratitis capitata, is a destructive agricultural pest with a long history of invasion success. This pest has been affecting different regions of the United States for the past 30 years, but a number of studies of medfly bioinfestations has focused on the situation in California. Although some progress has been made in terms of establishing the origin of infestations, the overall status of this pest in this area remains controversial. Specifically, do flies captured over the years represent independent infestations or the persistence of a resident population? We present an effort to answer this question based on the use of multilocus genotyping. Ten microsatellite loci were used to analyse 109 medflies captured in several infestations within California between 1992 and 1998. Using these same markers, 242 medflies from regions of the world having 'established' populations of this pest including Hawaii, Guatemala, El Salvador, Ecuador, Brazil, Argentina and Peru, were also analysed. Although phylogenetic analysis, amova analysis, the IMMANC assignment test and geneclass exclusion test analysis suggest that some of the medflies captured in California are derived from independent invasion events, analysis of specimens from the Los Angeles basin provides support for the hypothesis that an endemic population, probably derived from Guatemala, has been established.

  12. Microsatellite data support subpopulation structuring among Basques.

    Science.gov (United States)

    Pérez-Miranda, Ana M; Alfonso-Sánchez, Miguel A; Kalantar, Arif; García-Obregón, Susana; de Pancorbo, Marian M; Peña, José A; Herrera, Rene J

    2005-01-01

    Genomic diversity based on 13 short tandem repeat (STR) loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, TH01, TPOX, and CSF1PO) is reported for the first time in Basques from the provinces of Guipúzcoa and Navarre (Spain). STR data from previous studies on Basques from Alava and Vizcaya provinces were also examined using hierarchal analysis of molecular variance (AMOVA) and genetic admixture estimations to ascertain whether the Basques are genetically heterogeneous. To assess the genetic position of Basques in a broader geographic context, we conducted phylogenetic analyses based on F(ST) genetic distances [neighbor-joining trees and multidimensional scaling (MDS)] using data compiled in previous publications. The genetic profile of the Basque groups revealed distinctive regional partitioning of short tandem repeat (STR) diversity. Consistent with the above, native Basques clearly segregated from other populations from Europe (including Spain), North Africa, and the Middle East. The main line of genetic discontinuity inferred from the spatial variability of the microsatellite diversity in Basques significantly overlapped the geographic distribution of the Basque language. The genetic heterogeneity among native Basque groups correlates with the peculiar geography of peopling and marital structure in rural Basque zones and with language boundaries resulting from the uneven impact of Romance languages in the different Basque territories.

  13. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis

    NARCIS (Netherlands)

    B.F. Voight (Benjamin); L.J. Scott (Laura); V. Steinthorsdottir (Valgerdur); A.D. Morris (Andrew); C. Dina (Christian); R.P. Welch (Ryan); E. Zeggini (Eleftheria); C. Huth (Cornelia); Y.S. Aulchenko (Yurii); G. Thorleifsson (Gudmar); L.J. McCulloch (Laura); T. Ferreira (Teresa); H. Grallert (Harald); N. Amin (Najaf); G. Wu (Guanming); C.J. Willer (Cristen); S. Raychaudhuri (Soumya); S.A. McCarroll (Steven); C. Langenberg (Claudia); O.M. Hofmann (Oliver); J. Dupuis (Josée); L. Qi (Lu); A.V. Segrè (Ayellet); M. van Hoek (Mandy); P. Navarro (Pau); K.G. Ardlie (Kristin); B. Balkau (Beverley); R. Benediktsson (Rafn); A.J. Bennett (Amanda); R. Blagieva (Roza); E.A. Boerwinkle (Eric); L.L. Bonnycastle (Lori); K.B. Boström (Kristina Bengtsson); B. Bravenboer (Bert); S. Bumpstead (Suzannah); N.P. Burtt (Noël); G. Charpentier (Guillaume); P.S. Chines (Peter); M. Cornelis (Marilyn); D.J. Couper (David); G. Crawford (Gabe); A.S.F. Doney (Alex); K.S. Elliott (Katherine); M.R. Erdos (Michael); C.S. Fox (Caroline); C.S. Franklin (Christopher); M. Ganser (Martha); C. Gieger (Christian); N. Grarup (Niels); T. Green (Todd); S. Griffin (Simon); C.J. Groves (Christopher); C. Guiducci (Candace); S. Hadjadj (Samy); N. Hassanali (Neelam); C. Herder (Christian); B. Isomaa (Bo); A.U. Jackson (Anne); P.R.V. Johnson (Paul); T. Jørgensen (Torben); W.H.L. Kao (Wen); N. Klopp (Norman); A. Kong (Augustine); P. Kraft (Peter); J. Kuusisto (Johanna); T. Lauritzen (Torsten); M. Li (Man); A. Lieverse (Aloysius); C.M. Lindgren (Cecilia); V. Lyssenko (Valeriya); M. Marre (Michel); T. Meitinger (Thomas); K. Midthjell (Kristian); M.A. Morken (Mario); N. Narisu (Narisu); P. Nilsson (Peter); K.R. Owen (Katharine); F. Payne (Felicity); J.R.B. Perry (John); A.K. Petersen; C. Platou (Carl); C. Proença (Christine); I. Prokopenko (Inga); W. Rathmann (Wolfgang); N.W. Rayner (Nigel William); N.R. Robertson (Neil); G. Rocheleau (Ghislain); M. Roden (Michael); M.J. Sampson (Michael); R. Saxena (Richa); B.M. Shields (Beverley); P. Shrader (Peter); G. Sigurdsson (Gunnar); T. Sparsø (Thomas); K. Strassburger (Klaus); H.M. Stringham (Heather); Q. Sun (Qi); A.J. Swift (Amy); B. Thorand (Barbara); J. Tichet (Jean); T. Tuomi (Tiinamaija); R.M. van Dam (Rob); T.W. van Haeften (Timon); T.W. van Herpt (Thijs); J.V. van Vliet-Ostaptchouk (Jana); G.B. Walters (Bragi); M.N. Weedon (Michael); C. Wijmenga (Cisca); J.C.M. Witteman (Jacqueline); R.N. Bergman (Richard); S. Cauchi (Stephane); F.S. Collins (Francis); A.L. Gloyn (Anna); U. Gyllensten (Ulf); T. Hansen (Torben); W.A. Hide (Winston); G.A. Hitman (Graham); A. Hofman (Albert); D. Hunter (David); K. Hveem (Kristian); M. Laakso (Markku); K.L. Mohlke (Karen); C.N.A. Palmer (Colin); P.P. Pramstaller (Peter Paul); I. Rudan (Igor); E.J.G. Sijbrands (Eric); L.D. Stein (Lincoln); J. Tuomilehto (Jaakko); A.G. Uitterlinden (André); M. Walker (Mark); N.J. Wareham (Nick); G.R. Abecasis (Gonçalo); B.O. Boehm (Bernhard); H. Campbell (Harry); M.J. Daly (Mark); A.T. Hattersley (Andrew); F.B. Hu (Frank); J.B. Meigs (James); J.S. Pankow (James); O. Pedersen (Oluf); H.E. Wichmann (Erich); I. Barroso (Inês); J.C. Florez (Jose); T.M. Frayling (Timothy); L. Groop (Leif); R. Sladek (Rob); U. Thorsteinsdottir (Unnur); J.F. Wilson (James); T. Illig (Thomas); P. Froguel (Philippe); P. Tikka-Kleemola (Päivi); J-A. Zwart (John-Anker); D. Altshuler (David); M. Boehnke (Michael); M.I. McCarthy (Mark); R.M. Watanabe (Richard)

    2010-01-01

    textabstractBy combining genome-wide association data from 8,130 individuals with type 2 diabetes (T2D) and 38,987 controls of European descent and following up previously unidentified meta-analysis signals in a further 34,412 cases and 59,925 controls, we identified 12 new T2D association signals w

  14. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis

    NARCIS (Netherlands)

    Voight, Benjamin F.; Scott, Laura J.; Steinthorsdottir, Valgerdur; Morris, Andrew P.; Dina, Christian; Welch, Ryan P.; Zeggini, Eleftheria; Huth, Cornelia; Aulchenko, Yurii S.; Thorleifsson, Gudmar; McCulloch, Laura J.; Ferreira, Teresa; Grallert, Harald; Amin, Najaf; Wu, Guanming; Willer, Cristen J.; Raychaudhuri, Soumya; McCarroll, Steve A.; Langenberg, Claudia; Hofmann, Oliver M.; Dupuis, Josee; Qi, Lu; Segre, Ayellet V.; van Hoek, Mandy; Navarro, Pau; Ardlie, Kristin; Balkau, Beverley; Benediktsson, Rafn; Bennett, Amanda J.; Blagieva, Roza; Boerwinkle, Eric; Bonnycastle, Lori L.; Bostrom, Kristina Bengtsson; Bravenboer, Bert; Bumpstead, Suzannah; Burtt, Noisel P.; Charpentier, Guillaume; Chines, Peter S.; Cornelis, Marilyn; Couper, David J.; Crawford, Gabe; Doney, Alex S. F.; Elliott, Katherine S.; Elliott, Amanda L.; Erdos, Michael R.; Fox, Caroline S.; Franklin, Christopher S.; Ganser, Martha; Gieger, Christian; Grarup, Niels; Green, Todd; Griffin, Simon; Groves, Christopher J.; Guiducci, Candace; Hadjadj, Samy; Hassanali, Neelam; Herder, Christian; Isomaa, Bo; Jackson, Anne U.; Johnson, Paul R. V.; Jorgensen, Torben; Kao, Wen H. L.; Klopp, Norman; Kong, Augustine; Kraft, Peter; Kuusisto, Johanna; Lauritzen, Torsten; Li, Man; Lieverse, Aloysius; Lindgren, Cecilia M.; Lyssenko, Valeriya; Marre, Michel; Meitinger, Thomas; Midthjell, Kristian; Morken, Mario A.; Narisu, Narisu; Nilsson, Peter; Owen, Katharine R.; Payne, Felicity; Perry, John R. B.; Petersen, Ann-Kristin; Platou, Carl; Proenca, Christine; Prokopenko, Inga; Rathmann, Wolfgang; Rayner, N. William; Robertson, Neil R.; Rocheleau, Ghislain; Roden, Michael; Sampson, Michael J.; Saxena, Richa; Shields, Beverley M.; Shrader, Peter; Sigurdsson, Gunnar; Sparso, Thomas; Strassburger, Klaus; Stringham, Heather M.; Sun, Qi; Swift, Amy J.; Thorand, Barbara; Tichet, Jean; Tuomi, Tiinamaija; van Dam, Rob M.; van Haeften, Timon W.; van Herpt, Thijs; van Vliet-Ostaptchouk, Jana V.; Walters, G. Bragi; Weedon, Michael N.; Wijmenga, Cisca; Witteman, Jacqueline; Bergman, Richard N.; Cauchi, Stephane; Collins, Francis S.; Gloyn, Anna L.; Gyllensten, Ulf; Hansen, Torben; Hide, Winston A.; Hitman, Graham A.; Hofman, Albert; Hunter, David J.; Hveem, Kristian; Laakso, Markku; Mohlke, Karen L.; Morris, Andrew D.; Palmer, Colin N. A.; Pramstaller, Peter P.; Rudan, Igor; Sijbrands, Eric; Stein, Lincoln D.; Tuomilehto, Jaakko; Uitterlinden, Andre; Walker, Mark; Wareham, Nicholas J.; Watanabe, Richard M.; Abecasis, Goncalo R.; Boehm, Bernhard O.; Campbell, Harry; Daly, Mark J.; Hattersley, Andrew T.; Hu, Frank B.; Meigs, James B.; Pankow, James S.; Pedersen, Oluf; Wichmann, H-Erich; Barroso, Ines; Florez, Jose C.; Frayling, Timothy M.; Groop, Leif; Sladek, Rob; Thorsteinsdottir, Unnur; Wilson, James F.; Illig, Thomas; Froguel, Philippe; van Duijn, Cornelia M.; Stefansson, Kari; Altshuler, David; Boehnke, Michael; McCarthy, Mark I.

    2010-01-01

    By combining genome-wide association data from 8,130 individuals with type 2 diabetes (T2D) and 38,987 controls of European descent and following up previously unidentified meta-analysis signals in a further 34,412 cases and 59,925 controls, we identified 12 new T2D association signals with combined

  15. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis

    DEFF Research Database (Denmark)

    Voight, Benjamin F; Scott, Laura J; Steinthorsdottir, Valgerdur

    2010-01-01

    By combining genome-wide association data from 8,130 individuals with type 2 diabetes (T2D) and 38,987 controls of European descent and following up previously unidentified meta-analysis signals in a further 34,412 cases and 59,925 controls, we identified 12 new T2D association signals...

  16. Variation on DNA microsatellite of Holstein-Friesian dairy cows in Baturaden Dairy Cattle Breeding Center

    Directory of Open Access Journals (Sweden)

    C Sumantri

    2007-06-01

    Full Text Available Eight microsatellite loci of which the locations were three on chromosome 6 (BTA6 namely CSN 3, BM 143 and BM 415; two on chromosome 9 (BTA9 namely ETH 225 and BM 4208; and three on chromosome 10 (BTA10 namely BP 31, BM 1237 and BM 888 were used to investigate genotypic variation of Holstein-Friesian (HF dairy cows in Baturraden Dairy Cattle Breeding Centre. Research activities were carried out through some steps involving blood collection, DNA isolation, amplification on DNA fragments by polymerase chain reaction (PCR and separation by electrophoresis with silver staining. Frequency and heterozygosity of genes under consideration were calculated. The results showed that the eight microsatellite loci exhibited a total number of 33 alleles. Locations of those alleles were five in BM 143 and BM 4208 loci; four in BM 415, CSN 3, ETH 225, BM 1237, BM 888 loci; and three in BP 31 locus. A number of 14 out of 33 alleles might be specific alleles for HF dairy cattle in Baturraden Dairy Cattle Breeding Centre. The lowest heterozygosity per locus (ĥ was 0.6151 for BM 415 whilst the highest one was 0.7301 for BM 888. Additionally, the average heterozygosity for all loci (Ĥ detected in this study was 0.6768. The genotype BB on locus BM 143 and AC on locus CSN-3 significantly affected (P<0.05 the estimated breeding value of milk yield of HF cows in this location.

  17. Isolation and characterization of the first microsatellite markers for the southern harvester termite, Microhodotermes viator.

    Science.gov (United States)

    Muna, N; O'Ryan, C

    2016-08-01

    The southern harvester termite, Microhodotermes viator, is ecologically important due to its nutrient cycling activities and trophic interactions. Additionally, M. viator appears to have very long-lived colonies, which amplifies their effect on the environment. In order to estimate the longevity of a colony it is necessary to understand colony genetic structure. However, intra- and intercolonial genetic structure and levels of relatedness have not yet been examined in this species, likely due to a lack of microsatellite markers that effectively hybridize in this species. Here we describe the identification and characterization of seven microsatellite loci for M. viator, using an enriched approach and a preliminary test of their suitability for studies of fine-scale population genetic structure. Seven polymorphic loci were identified, none of which deviated from Hardy-Weinberg equilibrium. The loci had an average of 5.8 alleles per locus (range: 2-14) and an overall mean heterozygosity of 0.51 ± 0.3. Across all loci, population level pairwise F ST values showed significant genetic differentiation. The loci described and preliminary genetic data presented here provide an invaluable tool for future studies of population structure and longevity in M. viator colonies.

  18. Characterization of 15 tetranucleotide microsatellite markers in the ringtail (Bassariscus astutus).

    Science.gov (United States)

    Schweizer, Rena M; Roemer, Gary W; Pollinger, John P; Wayne, Robert K

    2009-01-01

    We characterized 15 polymorphic tetranucleotide microsatellite markers for the ringtail, Bassariscus astutus. We tested these loci in 21 individuals captured in Arizona and Texas and found six to 19 alleles per locus. Observed and expected heterozygosities ranged from 0.381 to 1.000 and from 0.381 to 0.941, respectively. All loci were in Hardy-Weinberg equilibrium, and none were in linkage disequilibrium. These markers may be used to investigate population genetics and mating patterns in this species.

  19. Boechera microsatellite website: an online portal for species identification and determination of hybrid parentage.

    Science.gov (United States)

    Li, Fay-Wei; Rushworth, Catherine A; Beck, James B; Windham, Michael D

    2017-01-01

    Boechera (Brassicaceae) has many features to recommend it as a model genus for ecological and evolutionary research, including species richness, ecological diversity, experimental tractability and close phylogenetic proximity to Arabidopsis . However, efforts to realize the full potential of this model system have been thwarted by the frequent inability of researchers to identify their samples and place them in a broader evolutionary context. Here we present the Boechera Microsatellite Website (BMW), a portal that archives over 55 000 microsatellite allele calls from 4471 specimens (including 133 nomenclatural types). The portal includes analytical tools that utilize data from 15 microsatellite loci as a highly effective DNA barcoding system. The BMW facilitates the accurate identification of Boechera samples and the investigation of reticulate evolution among the ±83 sexual diploid taxa in the genus, thereby greatly enhancing Boechera 's potential as a model system.

  20. [Increased variability of (TCC)n microsatelline loci in populations of the parthenogenetic lizard Lacerta unisexualis Darevsky].

    Science.gov (United States)

    Ryskov, A P; Kan, N G; Martirosian, I A; Darevskiĭ, I S; Danielian, F D; Petrosian, V G; Tokarskaia, O N

    2000-11-01

    In four isolated populations of parthenogenetic Caucasian rock lizard Lacerta unisexualis, variability of (TCC)n loci was examined using multilocus DNA fingerprinting. Unexpectedly high variability of (TCC)n microsatellites was found in all four populations. The mean similarity index was 0.825, which is higher than similarity estimates obtained for other mini- and microsatellite loci in L. unisexualis and parthenogenetic species L. dahli and L. armeniaca studied earlier. The high variation level of (TCC)n loci was shown to be at least partially associated with the presence of a diverged (TCC)n sequence fraction in the L. unisexualis genome. Mutations at some other genetically unstable (TCC)n loci may cause their structural diversity in populations of L. unisexualis.

  1. Isolation and characterization of novel microsatellite markers in pomegranate (Punica granatum L.).

    Science.gov (United States)

    Pirseyedi, Seyed Mostafa; Valizadehghan, Sahar; Mardi, Mohsen; Ghaffari, Mohammad Reza; Mahmoodi, Parvaneh; Zahravi, Mehdi; Zeinalabedini, Mehrshad; Nekoui, Seyed Mojtaba Khayam

    2010-05-03

    Pomegranate (Punica granatum L.) has been cultivated from ancient times for its economic, ornamental and medicinal properties globally. Here, we report the isolation and characterization of 12 polymorphic microsatellite markers from a repeat-enriched genomic library of Punica granatum L. The genetic diversity of these loci was assessed in 60 genotypes of Punica granatum L. All loci were variable: the number of polymorphic alleles per locus ranged from two to five (average 2.9). The observed and expected heterozygosities ranged from 0.15 to 0.87 and 0.29 to 0.65, respectively. The polymorphic information content ranged from 0.26 to 0.61 (average: 0.43). To the best of our knowledge, this is the first time that polymorphic microsatellite markers have been reported for P. granatum L. These new markers should allow studies of the population structure and genetic diversity of pomegranate to be performed in the future.

  2. Development and Characterization of Fifteen Polymorphic Microsatellites for Extremely Endangered Salamander, Echinotriton chinhaiensis

    Institute of Scientific and Technical Information of China (English)

    Weizhao YANG; Jie WANG; Jianping JIANG; Cheng LI; Feng XIE

    2014-01-01

    Echinotriton chinhaiensis is a critically endangered salamander and its distribution is restricted to Ningbo, Zhejiang Province of China. In this study, we developed and characterized iffteen polymorphic microsatellite loci forE. chinhaiensis from dinucleotide- and tetranucleotide- enriched library. The number of alleles ranges from 4 to 12 with an average of 7.27 alleles per locus. The observed and expected heterozygosities values were from 0.250 to 0.844 and 0.511 to 0.872 with an average value of 0.596 and 0.722; respectively. The polymorphic microsatellite loci described in this paper are useful in the further study on genetic diversity and gene lfow, which would be helpful to formulate effective conservation strategies for theE. chinhaiensis.

  3. Development of genomic microsatellites in Gleditsia triacanthos (Fabaceae) using Illumina sequencing1

    Science.gov (United States)

    Owusu, Sandra A.; Staton, Margaret; Jennings, Tara N.; Schlarbaum, Scott; Coggeshall, Mark V.; Romero-Severson, Jeanne; Carlson, John E.; Gailing, Oliver

    2013-01-01

    • Premise of the study: Fourteen genomic microsatellite markers were developed and characterized in honey locust, Gleditsia triacanthos, using Illumina sequencing. Due to their high variability, these markers can be applied in analyses of genetic diversity and structure, and in mating system and gene flow studies. • Methods and Results: Thirty-six individuals from across the species range were included in a genetic diversity analysis and yielded three to 20 alleles per locus. Observed heterozygosity and expected heterozygosity ranged from 0.214 to 0.944 and from 0.400 to 0.934, respectively, with minimal occurrence of null alleles. Regular segregation of maternal alleles was observed at seven loci and moderate segregation distortion at four of 11 loci that were heterozygous in the seed parent. • Conclusions: Honey locust is an important agroforestry tree capable of very fast growth and tolerance of poor site conditions. This is the first report of genomic microsatellites for this species. PMID:25202504

  4. Development of Genomic Microsatellites in Gleditsia triacanthos (Fabaceae Using Illumina Sequencing

    Directory of Open Access Journals (Sweden)

    Sandra A. Owusu

    2013-11-01

    Full Text Available Premise of the study: Fourteen genomic microsatellite markers were developed and characterized in honey locust, Gleditsia triacanthos, using Illumina sequencing. Due to their high variability, these markers can be applied in analyses of genetic diversity and structure, and in mating system and gene flow studies. Methods and Results: Thirty-six individuals from across the species range were included in a genetic diversity analysis and yielded three to 20 alleles per locus. Observed heterozygosity and expected heterozygosity ranged from 0.214 to 0.944 and from 0.400 to 0.934, respectively, with minimal occurrence of null alleles. Regular segregation of maternal alleles was observed at seven loci and moderate segregation distortion at four of 11 loci that were heterozygous in the seed parent. Conclusions: Honey locust is an important agroforestry tree capable of very fast growth and tolerance of poor site conditions. This is the first report of genomic microsatellites for this species.

  5. Development of genomic microsatellites in Gleditsia triacanthos (Fabaceae) using Illumina sequencing.

    Science.gov (United States)

    Owusu, Sandra A; Staton, Margaret; Jennings, Tara N; Schlarbaum, Scott; Coggeshall, Mark V; Romero-Severson, Jeanne; Carlson, John E; Gailing, Oliver

    2013-12-01

    Fourteen genomic microsatellite markers were developed and characterized in honey locust, Gleditsia triacanthos, using Illumina sequencing. Due to their high variability, these markers can be applied in analyses of genetic diversity and structure, and in mating system and gene flow studies. • Thirty-six individuals from across the species range were included in a genetic diversity analysis and yielded three to 20 alleles per locus. Observed heterozygosity and expected heterozygosity ranged from 0.214 to 0.944 and from 0.400 to 0.934, respectively, with minimal occurrence of null alleles. Regular segregation of maternal alleles was observed at seven loci and moderate segregation distortion at four of 11 loci that were heterozygous in the seed parent. • Honey locust is an important agroforestry tree capable of very fast growth and tolerance of poor site conditions. This is the first report of genomic microsatellites for this species.

  6. 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.

  7. Characterization of eight novel microsatellite markers in the green-lipped mussel Perna viridis (Mytilidae).

    Science.gov (United States)

    Cao, Y Y; Li, Z B; Li, Q H; Chen, X J; Chen, L; Dai, G

    2013-02-07

    The green lipped mussel, also known as the Asian green mussel (Perna viridis) is a fast reproducing and valuable food source, but it is also considered an invasive species and can clog and damage pipes and marine equipment. Eight novel polymorphic microsatellite loci for P. viridis were isolated and characterized. Microsatellite polymorphism was evaluated in 30 individuals collected from Xiamen, China. The number of alleles per locus and the polymorphism information content ranged from 2 to 5 and from 0.3092 to 0.7031, respectively. The observed and expected heterozygosities were 0.1538-0.8400 and 0.1448-0.6833, respectively. The loci identified in this study could provide a useful tool for the genetic population structure analysis of P. viridis.

  8. Microsatellite markers for Nuphar japonica (Nymphaeaceae), an aquatic plant in the agricultural ecosystem of Japan1

    Science.gov (United States)

    Kondo, Toshiaki; Watanabe, Sonoko; Shiga, Takashi; Isagi, Yuji

    2016-01-01

    Premise of the study: Nuphar species (Nymphaeaceae) are representative aquatic plants in irrigation ponds in Japanese agricultural ecosystems. We developed 15 polymorphic microsatellite markers for N. japonica and confirmed their utility for its close relatives N. oguraensis var. akiensis and N. ×saijoensis, which originated from natural hybridization between N. japonica and N. oguraensis. Methods and Results: Genetic variation was characterized in 15 polymorphic loci in three populations of N. japonica. The average number of alleles per locus was 3.47 (range = 2−9; n = 32), and the average expected heterozygosity per locus was 0.84 (range = 0.5–1.0); 11 loci were amplified in N. oguraensis var. akiensis and 15 in N. ×saijoensis. Conclusions: The polymorphic microsatellite markers developed in this study will be useful for investigating the levels of genetic diversity within remnant populations of Nuphar taxa and could provide a valuable tool for conservation genetics of these taxa. PMID:28101435

  9. Profile of candidate microsatellite markers in Sebastiscus marmoratus using 454 pyrosequencing

    Science.gov (United States)

    Song, Na; Chen, Muyan; Gao, Tianxiang; Yanagimoto, Takashi

    2017-01-01

    Sebastiscus marmoratus is an important sedentary ovoviparous fish distributed in near-shore coastal waters from the coast of China to Japan. Candidate S. marmoratus microsatellite markers were developed in the present study using 454 pyrosequencing, and the marker profile was analyzed. A total of 2 000 000 raw sequence reads were assembled to reduce redundancy. Among them, 1 043 dinucleotide, 925 trinucleotide, 692 tetranucleotide, and 315 pentanucleotide repeats were detected. AC repeats were the most frequent motifs among the dinucleotide repeats, and AAT was the most abundant among the trinucleotide repeats. AAAT, ATAG, and ATCC were the three most common tetranucleotide motifs, and AAGAT and AATAT were the most dominant pentanucleotide motifs. The greatest numbers of loci and potentially amplifiable loci were found in dinucleotide repeats, whereas trinucleotide repeats had the fewest. In summary, a wide range of candidate microsatellite markers were identified in the present study using a rapid and efficient 454 pyrosequencing approach.

  10. Development and Characterization of Microsatellite Markers for the Medicinal Plant Smilax brasiliensis (Smilacaceae and Related Species

    Directory of Open Access Journals (Sweden)

    Aline R. Martins

    2013-06-01

    Full Text Available Premise of the study: A new set of microsatellite or simple sequence repeat (SSR markers were developed for Smilax brasiliensis, which is popularly known as sarsaparilla and used in folk medicine as a tonic, antirheumatic, and antisyphilitic. Smilax brasiliensis is sold in Brazilian pharmacies, and its origin and effectiveness are not subject to quality control. Methods and Results: Using a protocol for genomic library enrichment, primer pairs were developed for 26 microsatellite loci and validated in 17 accessions of S. brasiliensis. Thirteen loci were polymorphic and four were monomorphic. The primers successfully amplified alleles in the congeners S. campestris, S. cissoides, S. fluminensis, S . goyazana, S. polyantha, S. quinquenervia, S. rufescens, S. subsessiliflora, and S. syphilitica. Conclusions: The new SSR markers described herein are informative tools for genetic diversity and gene flow studies in S. brasiliensis and several congeners.

  11. Microsatellite markers for Urochloa humidicola (Poaceae) and their transferability to other Urochloa species.

    Science.gov (United States)

    Santos, Jean C S; Barreto, Mariana A; Oliveira, Fernanda A; Vigna, Bianca B Z; Souza, Anete P

    2015-03-15

    Urochloa humidicola is a warm-season grass commonly used as forage in the tropics and is recognized for its tolerance to seasonal flooding. This grass is an important forage species for the Cerrado and Amazon regions of Brazil. U. humidicola is a polyploid species with variable ploidy (6X-9X) and facultative apomixis with high phenotypic plasticity. However, this apomixis and ploidy, as well as the limited knowledge of the genetic basis of the germplasm collection, have constrained genetic breeding activities, yet microsatellite markers may enable a better understanding of the species' genetic composition. This study aimed to develop and characterize new polymorphic microsatellite molecular markers in U. humidicola and to evaluate their transferability to other Urochloa species. A set of microsatellite markers for U. humidicola was identified from two new enriched genomic DNA libraries: the first library was constructed from a single sexual genotype and the second from a pool of eight apomictic genotypes selected on the basis of previous results. Of the 114 loci developed, 72 primer pairs presented a good amplification product, and 64 were polymorphic among the 34 genotypes tested. The number of bands per simple sequence repeat (SSR) locus ranged from 1 to 29, with a mean of 9.6 bands per locus. The mean polymorphism information content (PIC) of all loci was 0.77, and the mean discrimination power (DP) was 0.87. STRUCTURE analysis revealed differences among U. humidicola accessions, hybrids, and other Urochloa accessions. The transferability of these microsatellites was evaluated in four species of the genus, U. brizantha, U. decumbens, U. ruziziensis, and U. dictyoneura, and the percentage of transferability ranged from 58.33% to 69.44% depending on the species. This work reports new polymorphic microsatellite markers for U. humidicola that can be used for breeding programs of this and other Urochloa species, including genetic linkage mapping, quantitative trait

  12. Transcriptome-Derived Tetranucleotide Microsatellites and Their Associated Genes from the Giant Panda (Ailuropoda melanoleuca).

    Science.gov (United States)

    Song, Xuhao; Shen, Fujun; Huang, Jie; Huang, Yan; Du, Lianming; Wang, Chengdong; Fan, Zhenxin; Hou, Rong; Yue, Bisong; Zhang, Xiuyue

    2016-09-01

    Recently, an increasing number of microsatellites or simple sequence repeats (SSRs) have been found and characterized from transcriptomes. Such SSRs can be employed as putative functional markers to easily tag corresponding genes, which play an important role in biomedical studies and genetic analysis. However, the transcriptome-derived SSRs for giant panda (Ailuropoda melanoleuca) are not yet available. In this work, we identified and characterized 20 tetranucleotide microsatellite loci from a transcript database generated from the blood of giant panda. Furthermore, we assigned their predicted transcriptome locations: 16 loci were assigned to untranslated regions (UTRs) and 4 loci were assigned to coding regions (CDSs). Gene identities of 14 transcripts contained corresponding microsatellites were determined, which provide useful information to study the potential contribution of SSRs to gene regulation in giant panda. The polymorphic information content (PIC) values ranged from 0.293 to 0.789 with an average of 0.603 for the 16 UTRs-derived SSRs. Interestingly, 4 CDS-derived microsatellites developed in our study were also polymorphic, and the instability of these 4 CDS-derived SSRs was further validated by re-genotyping and sequencing. The genes containing these 4 CDS-derived SSRs were embedded with various types of repeat motifs. The interaction of all the length-changing SSRs might provide a way against coding region frameshift caused by microsatellite instability. We hope these newly gene-associated biomarkers will pave the way for genetic and biomedical studies for giant panda in the future. In sum, this set of transcriptome-derived markers complements the genetic resources available for giant panda.

  13. Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers.

    Science.gov (United States)

    Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel

    2016-01-01

    Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains.

  14. Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers.

    Directory of Open Access Journals (Sweden)

    Bénédicte Coupat-Goutaland

    Full Text Available Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM. Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis. They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains.

  15. A microsatellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus

    Directory of Open Access Journals (Sweden)

    Williams Emlyn R

    2006-09-01

    Full Text Available Abstract Background Eucalypts are the most widely planted hardwood trees in the world occupying globally more than 18 million hectares as an important source of carbon neutral renewable energy and raw material for pulp, paper and solid wood. Quantitative Trait Loci (QTLs in Eucalyptus have been localized on pedigree-specific RAPD or AFLP maps seriously limiting the value of such QTL mapping efforts for molecular breeding. The availability of a genus-wide genetic map with transferable microsatellite markers has become a must for the effective advancement of genomic undertakings. This report describes the development of a novel set of 230 EMBRA microsatellites, the construction of the first comprehensive microsatellite-based consensus linkage map for Eucalyptus and the consolidation of existing linkage information for other microsatellites and candidate genes mapped in other species of the genus. Results The consensus map covers ~90% of the recombining genome of Eucalyptus, involves 234 mapped EMBRA loci on 11 linkage groups, an observed length of 1,568 cM and a mean distance between markers of 8.4 cM. A compilation of all microsatellite linkage information published in Eucalyptus allowed us to establish the homology among linkage groups between this consensus map and other maps published for E. globulus. Comparative mapping analyses also resulted in the linkage group assignment of other 41 microsatellites derived from other Eucalyptus species as well as candidate genes and QTLs for wood and flowering traits published in the literature. This report significantly increases the availability of microsatellite markers and mapping information for species of Eucalyptus and corroborates the high conservation of microsatellite flanking sequences and locus ordering between species of the genus. Conclusion This work represents an important step forward for Eucalyptus comparative genomics, opening stimulating perspectives for evolutionary studies and

  16. Characterization of 10 microsatellite markers for the understorey Amazonian herb Heliconia acuminata.

    Science.gov (United States)

    Côrtes, M C; Gowda, V; Kress, W J; Bruna, E M; Uriarte, M

    2009-07-01

    We characterized 10 microsatellite loci for the plant Heliconia acuminata from the Biological Dynamics of Forest Fragments Project (Manaus, Brazil). Markers were screened in 61 individuals from one population and were found to be polymorphic with an average of eight alleles per locus. We found moderate to high levels of polymorphic information content, and observed and expected heterozygosities. All 10 markers are suitable for spatial genetic structure and parentage analyses and will be used for understanding H. acuminata dynamics across a fragmented landscape.

  17. Characterization of 14 microsatellite DNA markers for the tropical forest tree Virola surinamensis (Rol.) Warb. (Myristicaceae).

    Science.gov (United States)

    Draheim, Hope; Cui, Melissa; Dick, Christopher W

    2009-09-01

    Fourteen microsatellite DNA markers were developed for studies of gene flow in the Neotropical rain forest tree Virola surinamensis. The loci were unlinked and polymorphic in a sample of 21 individuals, with two to 10 alleles per locus and observed heterozygosity ranging from 0.14 to 0.76. The overall exclusion probability (0.997) indicates high resolution for parentage-based analyses of gene flow.

  18. Empirical evaluation reveals best fit of a logistic mutation model for human Y-chromosomal microsatellites.

    Science.gov (United States)

    Jochens, Arne; Caliebe, Amke; Rösler, Uwe; Krawczak, Michael

    2011-12-01

    The rate of microsatellite mutation is dependent upon both the allele length and the repeat motif, but the exact nature of this relationship is still unknown. We analyzed data on the inheritance of human Y-chromosomal microsatellites in father-son duos, taken from 24 published reports and comprising 15,285 directly observable meioses. At the six microsatellites analyzed (DYS19, DYS389I, DYS390, DYS391, DYS392, and DYS393), a total of 162 mutations were observed. For each locus, we employed a maximum-likelihood approach to evaluate one of several single-step mutation models on the basis of the data. For five of the six loci considered, a novel logistic mutation model was found to provide the best fit according to Akaike's information criterion. This implies that the mutation probability at the loci increases (nonlinearly) with allele length at a rate that differs between upward and downward mutations. For DYS392, the best fit was provided by a linear model in which upward and downward mutation probabilities increase equally with allele length. This is the first study to empirically compare different microsatellite mutation models in a locus-specific fashion.

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

    Directory of Open Access Journals (Sweden)

    Suping Feng

    2013-01-01

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

  20. Microsatellite analysis of Rosa damascena Mill. accessions reveals genetic similarity between genotypes used for rose oil production and old Damask rose varieties.

    Science.gov (United States)

    Rusanov, K; Kovacheva, N; Vosman, B; Zhang, L; Rajapakse, S; Atanassov, A; Atanassov, I

    2005-08-01

    Damask roses are grown in several European and Asiatic countries for rose oil production. Twenty-six oil-bearing Rosa damascena Mill. accessions and 13 garden Damask roses were assayed by molecular markers. Microsatellite genotyping demonstrated that R. damascena Mill. accessions from Bulgaria, Iran, and India and old European Damask rose varieties possess identical microsatellite profiles, suggesting a common origin. At the same time, the data indicated that modern industrial oil rose cultivation is based on a very narrow genepool and that oil rose collections contain many genetically identical accessions. The study of long-term vegetative propagation of the Damask roses also reveals high somatic stability for the microsatellite loci analyzed.

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

    Science.gov (United States)

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

    2012-02-01

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

  2. Molecular characterization of twenty polymorphic microsatellite markers in the polyploid fruit tree species Syzygium samarangense (Myrtaceae).

    Science.gov (United States)

    Lai, J M; Tsai, C C; Yen, C R; Ko, Y Z; Chen, S R; Weng, I S; Lin, Y S; Chiang, Y C

    2015-10-21

    Syzygium samarangense (Blume) Merr. & Perry (wax apple) is an important commercial fruit tree in Southeast Asia. Here, microsatellite markers were developed to evaluate genetic diversity and distinguish cultivars in this species. In total, 161 microsatellite loci with sufficient flanking sequences to design primer sets were isolated from wax apple using a magnetic bead-enrichment method. Fifty-eight primer sets were designed based on the flanking sequences of each single sequence repeat (SSR) locus and were tested using 14 wax apple cultivars/lines. Twenty SSR loci were found to be polymorphic and transferable across the 14 wax apple cultivars/lines. The number of alleles and effective number of alleles detected per locus ranged from 4 to 12 and from 1.697 to 9.800, respectively. The expected heterozygosity ranged from 0.150 to 0.595 (mean = 0.414). Polymorphism information content values ranged from 0.502 to 0.866 (mean = 0.763). These new microsatellite loci will be of value for characterization of genetic diversity in wax apples and for the identification of cultivars.

  3. Transcriptome-derived microsatellite markers for Dioon (Zamiaceae) cycad species1

    Science.gov (United States)

    Prado, Alberto; Cervantes-Díaz, Fret; Perez-Zavala, Francisco G.; González-Astorga, Jorge; Bede, Jacqueline C.; Cibrián-Jaramillo, Angélica

    2016-01-01

    Premise of the study: Dioon (Zamiaceae) is an endangered North American cycad genus of evolutionary and ornamental value. We designed and validated a set of microsatellite markers from D. edule that can be used for population-level and conservation studies, and that transferred successfully to D. angustifolium, D. spinulosum, and D. holmgrenii. Methods and Results: We tested 50 primers from 80 microsatellite candidate loci in the OneKP D. edule transcriptome. Genotypes from 21 loci in 20 D. edule individuals revealed up to 14 alleles per locus and observed heterozygosity from 0.15 to 0.92; one locus was monomorphic. Seven of those 21 loci were polymorphic in D. angustifolium, D. spinulosum, and D. holmgrenii, with up to seven alleles, and an observed heterozygosity up to 0.89. Conclusions: The transcriptome-derived microsatellites generated here will serve as tools to advance population genetic studies and inform conservation strategies of Dioon, including the identification and origin of illegal plants in the cycad trade. PMID:26949574

  4. Development of novel microsatellite DNA markers by cross-amplification and analysis of genetic variation in gerbils.

    Science.gov (United States)

    Du, Xiaoyan; Chen, Zhenwen; Li, Wei; Tan, Yuanqing; Lu, Jing; Zhu, Xiangdong; Zhao, Taiyun; Dong, Gang; Zeng, Lin

    2010-01-01

    The objectives of this study are to establish microsatellite loci for the Mongolian gerbil based on mouse microsatellite DNA sequences and to investigate genetic variation in the laboratory gerbil (Capital Medical University, CMU) and 2 wild gerbil populations (from Yin Chuan city [YIN] and the Hohehot Municipality [HOH]). In total, 536 mouse microsatellite markers were chosen to identify polymorphic dinucleotide repeat loci in the gerbil by cross-amplification. Of these markers, 313 (58.39%) have been discretely amplified from the CMU laboratory gerbil and been sequenced. Of the 313 sequenced markers, 130 were confirmed as simple sequence repeat (SSR) loci in the gerbil. In total, 6 of those newly identified loci plus 6 identified in previous reports were used to estimate the genetic polymorphism for 30 laboratory gerbils and 54 wild gerbils (27 each of the HOH and YIN groups). A total of 29 alleles were observed in the 3 populations, and 11 of 12 loci (91.67%) are polymorphic markers. Nei's standard genetic distances of 0.0592 (CMU vs. HOH) and 0.1033 (CMU vs. YIN) were observed. The averages of observed versus expected heterozygosity are 0.5231/0.4008, 0.5051/0.3882, and 0.4825/0.3665 for the YIN, HOH, and CMU populations, respectively. These results show that cross-amplification using mouse microsatellite primers is an efficient way to identify gerbil SSR loci. By using these 12 selected markers, we have demonstrated that genetic variation level within the CMU population is higher than that has been reported previously and are comparable with the levels found in 2 wild populations.

  5. Microsatellite instability at tetranucleotide repeats in sporadic colorectal cancer in Japan.

    Science.gov (United States)

    Yamada, Kanae; Kanazawa, Shinsaku; Koike, Junichi; Sugiyama, Hisahiko; Xu, Can; Funahashi, Kimihiko; Boland, C Richard; Koi, Minoru; Hemmi, Hiromichi

    2010-02-01

    Most tumors of patients with Lynch syndrome and a fraction of sporadic colorectal cancers (CRCs) exhibit high levels of microsatellite instability (MSI) at mono- and dinucleotide repeat loci. A different type of instability, elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) has been found in non-colonic cancers. Our previous study demonstrated that EMAST is common in sporadic CRC. Here, we focused on the relationships between EMAST and other genomic instability parameters or clinicopathological features in an unselected series of 88 sporadic CRCs. Of the tumors in the sample, 4 (4.5%) were MSI-high (MSI-H), 9 (10.2%) were MSI-low (MSI-L) and 75 (85.2%) were microsatellite stable. EMAST status was determined using 7 EMAST markers. Fifty-three (60.2%) tumors without MSI-H showed instability at >or=1 EMAST loci. All 4 MSI-H tumors showed instability at several EMAST loci. Instability profiles of MSI-H tumors at EMAST loci were more complex than those of non-MSI-H tumors. A tendency of positive association was observed between MSI-L and EMAST (P=0.023). The frequency of loss of heterozygosity (LOH) for the 14 loci in EMAST-positive tumors was significantly higher than negative tumors (P=0.048). Among the clinicopathological parameters, only tumor location at the distal colon was associated with EMAST-negative tumors (P=0.0084, one-tailed). A relatively higher frequency of well-differentiated adenocarcinomas was observed in EMAST tumors as opposed to non-EMAST tumors, though the survival rate was similar. These results suggest that overlapping mechanisms that cause MSI-L, EMAST and LOH in CRCs may exist.

  6. Microsatellite Instability in Intestinal Metaplasia and Gastric Cancer

    Institute of Scientific and Technical Information of China (English)

    SHAOYun; ZHANGXiao-yong; LIUPing

    2004-01-01

    To investigate the changeable patterns of microsatellite instability(MSI)in intestinal metaplasia(IM)and gastric cancer(GC)and the role of MSI in gastric carcinogenesis. Methods: Silver staining single strand confornmtion polymorphism-polymeriase chain reaction(PCR-SSCP)wus used to screen MSI nmrkers at 5 loci in formalin-fixed, paraffin-embedded tissues of GC ( n = 30), IM ( n = 40) and corresponding normal gastric tissues. Resu/ts: The abnormal shifting of the single-strand DNA was identified in 7 (23.3%) out of GC and in 8 (20%) out of IM samples. Three ( 10 % ) tumors and one ( 2.5 % ) IM displayed high- frequency MSI ( two or more loci altered ). Low- frequencySI(one loci altered) was detected in 4( 13.3% )of the tmnors and in 7( 17.5% ) IM samples. GC with MSI was associated with distal location of the tumors but age,sex, differenl~ation, lymph nodes metastasis and TNM stage( P = 0.044).MSI was more likely detected in moderate-grade IM than in mild, grade IM tissues(34.8% versus 0; P = 0.013) ; and MSI had a tendency to be easily detected in female with IM. Conc/u,6~ : The progressive accmnulation of MSI in areas ofIM may contribute to GC development, represen~_g an importmlt molecular event in the multistep gastric ~~.

  7. Novel microsatellite markers acquired from Rubus coreanus Miq. and cross-amplification in other Rubus species.

    Science.gov (United States)

    Lee, Gi-An; Song, Jae Young; Choi, Heh-Ran; Chung, Jong-Wook; Jeon, Young-Ah; Lee, Jung-Ro; Ma, Kyung-Ho; Lee, Myung-Chul

    2015-04-10

    The Rubus genus consists of more than 600 species that are distributed globally. Only a few Rubus species, including raspberries and blueberries, have been domesticated. Genetic diversity within and between Rubus species is an important resource for breeding programs. We developed genomic microsatellite markers using an SSR-enriched R. coreanus library to study the diversity of the Rubus species. Microsatellite motifs were discovered in 546 of 646 unique clones, and a dinucleotide repeat was the most frequent (75.3%) type of repeat. From 97 microsatellite loci with reproducible amplicons, we acquired 29 polymorphic microsatellite markers in the Rubus coreanus collection. The transferability values ranged from 59.8% to 84% across six Rubus species, and Rubus parvifolius had the highest transferability value (84%). The average number of alleles and the polymorphism information content were 5.7 and 0.541, respectively, in the R. coreanus collection. The diversity index of R. coreanus was similar to the values reported for other Rubus species. A phylogenetic dendrogram based on SSR profiles revealed that seven Rubus species could be allocated to three groups, and that R. coreanus was genetically close to Rubus crataegifolius (mountain berry). These new microsatellite markers might prove useful in studies of the genetic diversity, population structure, and evolutionary relationships among Rubus species.

  8. Novel Microsatellite Markers Acquired from Rubus coreanus Miq. and Cross-Amplification in Other Rubus Species

    Directory of Open Access Journals (Sweden)

    Gi-An Lee

    2015-04-01

    Full Text Available The Rubus genus consists of more than 600 species that are distributed globally. Only a few Rubus species, including raspberries and blueberries, have been domesticated. Genetic diversity within and between Rubus species is an important resource for breeding programs. We developed genomic microsatellite markers using an SSR-enriched R. coreanus library to study the diversity of the Rubus species. Microsatellite motifs were discovered in 546 of 646 unique clones, and a dinucleotide repeat was the most frequent (75.3% type of repeat. From 97 microsatellite loci with reproducible amplicons, we acquired 29 polymorphic microsatellite markers in the Rubus coreanus collection. The transferability values ranged from 59.8% to 84% across six Rubus species, and Rubus parvifolius had the highest transferability value (84%. The average number of alleles and the polymorphism information content were 5.7 and 0.541, respectively, in the R. coreanus collection. The diversity index of R. coreanus was similar to the values reported for other Rubus species. A phylogenetic dendrogram based on SSR profiles revealed that seven Rubus species could be allocated to three groups, and that R. coreanus was genetically close to Rubus crataegifolius (mountain berry. These new microsatellite markers might prove useful in studies of the genetic diversity, population structure, and evolutionary relationships among Rubus species.

  9. Expression pattern and polymorphism of three microsatellite markers in the porcine CA3 gene

    Directory of Open Access Journals (Sweden)

    Zheng Rong

    2008-03-01

    Full Text Available Abstract Carbonic anhydrase III (CA3 is an abundant muscle protein characteristic of adult type-1, slow-twitch, muscle fibres. In order to further understand the functions of the porcine CA3 protein in muscle, the temporal and spatial distributions of its gene product were analysed and the association between the presence of specific polymorphisms and carcass traits in the pig was also examined. Real-time PCR revealed that the CA3 mRNA expression showed no differences with age in skeletal muscles from Yorkshire pigs at postnatal day-1, month-2, and month-4. We provide the first evidence that CA3 is differentially expressed in the skeletal muscle of Yorkshire and Meishan pig breeds. In addition, the whole pig genomic DNA sequence of CA3 was investigated and shown to contain seven exons and six introns. Comparative sequencing of the gene from three pig breeds revealed the existence of microsatellite SJ160 in intron 5 and microsatellite SJ158 and a novel microsatellite marker that includes a tandem repeat of (TCn in intron 4. We also determined the allele number and frequencies of the three loci in seven pig breeds and found that they are low polymorphic microsatellite markers. Statistical analysis showed that the CA3 microsatellite polymorphism was associated with dressing percentage, internal fat rate, carcass length, rib number and backfat thickness in the pig.

  10. Microsatellite abundance across the Anthozoa and Hydrozoa in the phylum Cnidaria.

    Science.gov (United States)

    Ruiz-Ramos, Dannise V; Baums, Iliana B

    2014-10-27

    Microsatellite loci have high mutation rates and thus are indicative of mutational processes within the genome. By concentrating on the symbiotic and aposymbiotic cnidarians, we investigated if microsatellite abundances follow a phylogenetic or ecological pattern. Individuals from eight species were shotgun sequenced using 454 GS-FLX Titanium technology. Sequences from the three available cnidarian genomes (Nematostella vectensis, Hydra magnipapillata and Acropora digitifera) were added to the analysis for a total of eleven species representing two classes, three subclasses and eight orders within the phylum Cnidaria. Trinucleotide and tetranucleotide repeats were the most abundant motifs, followed by hexa- and dinucleotides. Pentanucleotides were the least abundant motif in the data set. Hierarchical clustering and log likelihood ratio tests revealed a weak relationship between phylogeny and microsatellite content. Further, comparisons between cnidaria harboring intracellular dinoflagellates and those that do not, show microsatellite coverage is higher in the latter group. Our results support previous studies that found tri- and tetranucleotides to be the most abundant motifs in invertebrates. Differences in microsatellite coverage and composition between symbiotic and non-symbiotic cnidaria suggest the presence/absence of dinoflagellates might place restrictions on the host genome.

  11. Physical mapping of 49 microsatellite markers on chromosome 19 and correlation with the genetic linkage map

    Energy Technology Data Exchange (ETDEWEB)

    Reguigne-Arnould, I.; Mollicone, R.; Candelier, J.J. [INSERM, Villejuif (France)] [and others

    1996-03-05

    We have regionally localized 49 microsatellite markers developed by Genethon using a panel of previously characterized somatic cell hybrids that retain fragments from chromosome 19. The tight correlation observed between the physical and the genetic orders of the microsatellites provide cytogenetic anchorages to the genetic map data. We propose a position for the centromere just above D19S415, from the study of two hybrids, each of which retains one of the two derivatives of a balanced translocation t(1;19)(q11;q11). Microsatellites, which can be identified by a standard PCR protocol, are useful tools for the localization of disease genes and for the establishment of YAC or cosmid contigs. These markers can also judiciously be used for the characterization of new hybrid cell line panels. We report such a characterization of 11 clones, 8 of which were obtained by irradiation-fusion. Using the whole hybrid panel, we were able to define the order of 12 pairs of genetically colocalized microsatellites. As examples of gene mapping by the combined use of microsatellites and hybrid cell lines, we regionally assigned the PVS locus between the 19q13.2 markers D19S417 and D19S423 and confirmed the locations of fucosyltransferase loci FUT1, FUT2, and FUT5. 13 refs., 1 fig.

  12. High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries.

    Science.gov (United States)

    Malausa, Thibaut; Gilles, André; Meglécz, Emese; Blanquart, Hélène; Duthoy, Stéphanie; Costedoat, Caroline; Dubut, Vincent; Pech, Nicolas; Castagnone-Sereno, Philippe; Délye, Christophe; Feau, Nicolas; Frey, Pascal; Gauthier, Philippe; Guillemaud, Thomas; Hazard, Laurent; Le Corre, Valérie; Lung-Escarmant, Brigitte; Malé, Pierre-Jean G; Ferreira, Stéphanie; Martin, Jean-François

    2011-07-01

    Microsatellites (or SSRs: simple sequence repeats) are among the most frequently used DNA markers in many areas of research. The use of microsatellite markers is limited by the difficulties involved in their de novo isolation from species for which no genomic resources are available. We describe here a high-throughput method for isolating microsatellite markers based on coupling multiplex microsatellite enrichment and next-generation sequencing on 454 GS-FLX Titanium platforms. The procedure was calibrated on a model species (Apis mellifera) and validated on 13 other species from various taxonomic groups (animals, plants and fungi), including taxa for which severe difficulties were previously encountered using traditional methods. We obtained from 11,497 to 34,483 sequences depending on the species and the number of detected microsatellite loci ranged from 199 to 5791. We thus demonstrated that this procedure can be readily and successfully applied to a large variety of taxonomic groups, at much lower cost than would have been possible with traditional protocols. This method is expected to speed up the acquisition of high-quality genetic markers for nonmodel organisms.

  13. Comparative analysis of twelve Dothideomycete plant pathogens

    Energy Technology Data Exchange (ETDEWEB)

    Ohm, Robin; Aerts, Andrea; Salamov, Asaf; Goodwin, Stephen B.; Grigoriev, Igor

    2011-03-11

    The Dothideomycetes are one of the largest and most diverse groups of fungi. Many are plant pathogens and pose a serious threat to agricultural crops grown for biofuel, food or feed. Most Dothideomycetes have only a single host and related Dothideomycete species can have very diverse host plants. Twelve Dothideomycete genomes have currently been sequenced by the Joint Genome Institute and other sequencing centers. They can be accessed via Mycocosm which has tools for comparative analysis

  14. Variance-component analysis of obesity in Type 2 Diabetes confirms loci on chromosomes 1q and 11q

    NARCIS (Netherlands)

    Haeften, T.W. van; Pearson, P.L.; Tilburg, J.H.O. van; Strengman, E.; Sandkuijl, L.A.; Wijmenga, C.

    To study genetic loci influencing obesity in nuclear families with type 2 diabetes, we performed a genome-wide screen with 325 microsatellite markers that had an average spacing of 11 cM and a mean heterozygosity of ~75% covering all 22 autosomes. Genotype data were obtained from 562

  15. Identification of quantitative trait loci for wool traits in Iranian Baluchi sheep. Indian Journal of Animal Sciences

    DEFF Research Database (Denmark)

    Dashab, G R; Aslaminejad, A; Nassiri, M R;

    2012-01-01

    Regions on 3 ovine chromosomes (OAR1, 5 and 25) were selected to study quantitative trait loci (QTL) segregating for wool traits in Baluchi sheep, an indigenous sheep breed in Iran. Progenies (503) from 13 half-sib families were genotyped for 15 microsatellite markers. The average number of proge...

  16. Variance-component analysis of obesity in Type 2 Diabetes confirms loci on chromosomes 1q and 11q

    NARCIS (Netherlands)

    Haeften, T.W. van; Pearson, P.L.; Tilburg, J.H.O. van; Strengman, E.; Sandkuijl, L.A.; Wijmenga, C.

    2003-01-01

    To study genetic loci influencing obesity in nuclear families with type 2 diabetes, we performed a genome-wide screen with 325 microsatellite markers that had an average spacing of 11 cM and a mean heterozygosity of ~75% covering all 22 autosomes. Genotype data were obtained from 562 individuals fro

  17. Balancing selection maintains polymorphisms at neurogenetic loci in field experiments.

    Science.gov (United States)

    Lonn, Eija; Koskela, Esa; Mappes, Tapio; Mokkonen, Mikael; Sims, Angela M; Watts, Phillip C

    2017-04-04

    Most variation in behavior has a genetic basis, but the processes determining the level of diversity at behavioral loci are largely unknown for natural populations. Expression of arginine vasopressin receptor 1a (Avpr1a) and oxytocin receptor (Oxtr) in specific regions of the brain regulates diverse social and reproductive behaviors in mammals, including humans. That these genes have important fitness consequences and that natural populations contain extensive diversity at these loci implies the action of balancing selection. In Myodes glareolus, Avpr1a and Oxtr each contain a polymorphic microsatellite locus located in their 5' regulatory region (the regulatory region-associated microsatellite, RRAM) that likely regulates gene expression. To test the hypothesis that balancing selection maintains diversity at behavioral loci, we released artificially bred females and males with different RRAM allele lengths into field enclosures that differed in population density. The length of Avpr1a and Oxtr RRAMs was associated with reproductive success, but population density and the sex interacted to determine the optimal genotype. In general, longer Avpr1a RRAMs were more beneficial for males, and shorter RRAMs were more beneficial for females; the opposite was true for Oxtr RRAMs. Moreover, Avpr1a RRAM allele length is correlated with the reproductive success of the sexes during different phases of reproduction; for males, RRAM length correlated with the numbers of newborn offspring, but for females selection was evident on the number of weaned offspring. This report of density-dependence and sexual antagonism acting on loci within the arginine vasopressin-oxytocin pathway explains how genetic diversity at Avpr1a and Oxtr could be maintained in natural populations.

  18. Development of novel microsatellite markers for the Northern Goshawk (Accipiter gentilis) and their utility in cross-species amplification

    Science.gov (United States)

    Haughey, Christy; Sage, George K.; Degange, Gabriel; Sonsthagen, Sarah A.; Talbot, Sandra

    2016-01-01

    The Northern Goshawk (Accipiter gentilis) is a large forest raptor with a Holarctic distribution and, in some portions of its range, a species of conservation concern. To augment previously reported genetic markers, 13 novel polymorphic microsatellite markers were developed to establish individual identification and familial relationships, to assess levels of genetic diversity, and to identify diagnostic markers. Of the 22 loci tested, 13 were polymorphic, seven were monomorphic, and two failed to amplify. This suite of microsatellite loci yielded a combined probability of parental exclusion of 98%; a single individual sampled from a North American population can be reliably identified using a combination of seven of the 13 polymorphic loci. Cross-species screening in Cooper's Hawks (A. cooperii) and Sharp-shinned Hawks (A. striatus) of the 20 loci that successfully amplified in Northern Goshawks identified 13 loci as polymorphic in each species. Six of these loci (Age1303, Age1308, Age1309, Age1312, and Age1314) appeared to be useful in distinguishing between Accipiter species. These markers will be useful to researchers investigating populations of North American accipiters.

  19. Characterization of polymorphic microsatellites in the giant bulldog ant, Myrmecia brevinoda and the jumper ant, M. pilosula.

    Science.gov (United States)

    Qian, Zeng-Qiang; Ceccarelli, F Sara; Carew, Melissa E; Schlüns, Helge; Schlick-Steiner, Birgit C; Steiner, Florian M

    2011-01-01

    The ant genus Myrmecia Fabricius (Hymenoptera: Formicidae) is endemic to Australia and New Caledonia, and has retained many biological traits that are considered to be basal in the family Formicidae. Here, a set of 16 dinucleotide microsatellite loci were studied that are polymorphic in at least one of the two species of the genus: the giant bulldog ant, M. brevinoda Forel, and the jumper ant, M. pilosula Smith; 13 are novel loci and 3 are loci previously published for the genus Nothomyrmecia Clark (Hymenoptera: Formicidae). In M. brevinoda, the total of 12 polymorphic microsatellites yielded a total of 125 alleles, ranging from 3 to 18 with an average of 10.42 per locus; the observed and expected heterozygosities ranged from 0.4000 to 0.9000 and from 0.5413 to 0.9200, respectively. In M. pilosula, the 9 polymorphic loci yielded a total of 67 alleles, ranging from 3 to 12 with an average of 7.44 per locus; the observed and expected heterozygosities ranged from 0.5625 to 0.9375 and from 0.4863 to 0.8711, respectively. Five loci were polymorphic in both target species. In addition, 15 out of the 16 loci were successfully amplified in M. pyriformis. These informative microsatellite loci provide a powerful tool for investigating the population and colony genetic structure of M. brevinoda and M. pilosula, and may also be applicable to a range of congeners considering the relatively distant phylogenetic relatedness between M. pilosula and the other two species within the genus Myrmecia.

  20. Development of microsatellite markers in Garcinia paucinervis (Clusiaceae), an endangered species of karst habitats1

    Science.gov (United States)

    Hu, Gang; Zhang, Zhong-Hua; Yang, Ping; Zhang, Qi-Wei; Yuan, Chang-An

    2017-01-01

    Premise of the study: Microsatellite markers were developed for Garcinia paucinervis (Clusiaceae), an endangered and endemic tree species of karst habitats, to analyze its genetic diversity and genetic structure. Methods and Results: Using shotgun sequencing on an Illumina MiSeq platform, a total of 22 microsatellite primer sets were characterized, of which 17 were identified as polymorphic. For these polymorphic loci, the total number of alleles per locus ranged from two to 12 across 54 individuals from three populations. The observed and expected heterozygosities ranged from 0.000 to 1.000 and from 0.000 to 0.850, respectively. No pair of loci showed significant linkage disequilibrium. Three loci in one population deviated significantly from Hardy–Weinberg equilibrium (P < 0.05). Seven loci (JSL3, JSL5, JSL22, JSL29, JSL32, JSL39, and JSL43) were successfully amplified in G. bracteata. Conclusions: These markers will be useful in studies on genetic diversity and population structure of G. paucinervis. PMID:28090413

  1. A novel microsatellite control system

    Energy Technology Data Exchange (ETDEWEB)

    Moore, K.R.; Frigo, J.R.; Tilden, M.W.

    1998-02-01

    The authors are researching extremely simple yet quite capable analog pulse-coded neural networks for ``smaller-faster-cheaper`` spacecraft attitude and control systems. The will demonstrate a prototype microsatellite that uses their novel control method to autonomously stabilize itself in the ambient magnetic field and point itself at the brightest available light source. Though still in design infancy, the ``Nervous Net`` controllers described could allow for space missions not currently possible given conventional satellite hardware. Result, prospects and details are presented.

  2. Isolation and characterization of microsatellite markers for the tree-root endophytes Phialocephala subalpina and Phialocephala fortinii s.s.

    Science.gov (United States)

    Queloz, Valentin; Duò, Angelo; Grünig, Christoph R

    2008-11-01

    Species of the Phialocephala fortinii s.l.-Acephala applanata complex are the dominant dark septate endophytes (DSE) in roots of species belonging to the Pinaceae. The two species Phialocephala subalpina and P. fortinii s.s. belong to the most widely distributed species within this complex. In the present study, 15 polymorphic microsatellite loci were developed for these two closely related species. Strains of a community which were analysed previously using single-copy restriction fragment length polymorphism were screened with the new markers. Microsatellites were suitable to classify the two species and to recognize individuals within species.

  3. Identification and characterization of genic microsatellites in Cunninghamia lanceolata (Lamb. Hook (Taxodiaceae

    Directory of Open Access Journals (Sweden)

    Xu Yang

    2016-01-01

    Full Text Available Genomic resources for conventional breeding programs are extremely limited for coniferous trees, and existing simple sequence repeat markers are usually identified through the laborious process of hybridization screening. Therefore, this study aimed to identify gene-based microsatellites in the Chinese fir, Cunninghamia lanceolata (Lamb. Hook by screening transcript data. We identified 5200 microsatellites. Trinucleotide motifs were most common (47.94% and were followed by tetranucleotide motifs (24.92%. The AG/CT motif (43.93% was the most abundant dinucleotide repeat, whereas AAG/CTT (25.07% was the most common trinucleotide repeat. A total of 411 microsatellite primer pairs were designed and 97 polymorphic loci were identified by 8 genotypes. The number of alleles per locus (Na in these polymorphic loci ranged from 2 to 5 (mean, 2.640, the Ho values were 0.000-1.000 (mean, 0.479, and the HE values were 0.125-0.775 (mean, 0.462. The polymorphic information content (PIC values were 0.110-0.715 (mean, 0.383. Seventy-two of the 97 polymorphic markers (74.23% were present within genes with predicted functions. In addition, in genetic diversity and segregation analyses of 16 genotypes, only 5.88% of the polymorphic loci displayed segregation distortion at the p<0.05 level. Transferable amplification of a randomly selected set of 30 genic microsatellites showed that transferability decreased with increasing evolutionary distance between C. lanceolata and target conifers. Thus, these 97 genic markers will be useful for genetic diversity analysis, germplasm characterization, genome mapping and marker-assisted breeding in C. lanceolata, and evolutionary genetic analysis in Taxodiaceae.

  4. Newborn genetic identification: a protocol using microsatellite DNA as an alternative to footprinting.

    Science.gov (United States)

    de Pancorbo, M M; Rodríguez-Alarcón, J; Castro, A; Fernández-Fernández, I; Melchor, J C; Linares, A; García-Orad, A; Fernández-Llebrez del Rey, L; Aranguren, G; Santillana, L

    1997-07-04

    Newborn identification by foot- or finger-printing presents serious drawbacks. This study proposes an alternative method based on DNA analysis of blood-spots taken from the newborn child. CSF1PO, TPOX and TH01 microsatellite loci were chosen to develop a fast and reliable protocol to be applied in cases where it is suspected that newborn children have been exchanged. The advantage of these loci is that one can simultaneously amplify them by PCR multiplex reaction and determine their alleles, thereby reducing the time needed for identification tests. Moreover, the amplification products of these loci are very small (< 350 bp) and so can be analyzed in samples with degraded DNA. We have been able to prove that it is possible to obtain results in blood-spots taken from newborns up to 13 years before and kept at room temperature. Thus the protocol proposed here can be applied in long-term post-natal identification cases.

  5. Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences1

    Science.gov (United States)

    Gardner, Elliot M.; Laricchia, Kristen M.; Murphy, Matthew; Ragone, Diane; Scheffler, Brian E.; Simpson, Sheron; Williams, Evelyn W.; Zerega, Nyree J. C.

    2015-01-01

    Premise of the study: Chloroplast microsatellite loci were characterized from transcriptomes of Artocarpus altilis (breadfruit) and A. camansi (breadnut). They were tested in A. odoratissimus (terap) and A. altilis and evaluated in silico for two congeners. Methods and Results: Fifteen simple sequence repeats (SSRs) were identified in chloroplast sequences from four Artocarpus transcriptome assemblies. The markers were evaluated using capillary electrophoresis in A. odoratissimus (105 accessions) and A. altilis (73). They were also evaluated in silico in A. altilis (10), A. camansi (6), and A. altilis × A. mariannensis (7) transcriptomes. All loci were polymorphic in at least one species, with all 15 polymorphic in A. camansi. Per species, average alleles per locus ranged between 2.2 and 2.5. Three loci had evidence of fragment-length homoplasy. Conclusions: These markers will complement existing nuclear markers by enabling confident identification of maternal and clone lines, which are often important in vegetatively propagated crops such as breadfruit. PMID:26421253

  6. Sixteen EST-linked microsatellite markers in Günther's walking catfish, Clarias macrocephalus.

    Science.gov (United States)

    Sukkorntong, Chantapim; Panprommin, Dutrudi; Poompuang, Supawadee

    2008-11-01

    Twenty-seven new microsatellite sequences were identified by screening 2029 expressed sequence tags from Günther's walking catfish, Clarias macrocephalus. Sixteen loci were polymorphic with the number of alleles ranging from two to 16 per locus and the observed and expected heterozygosities ranging from 0.4667 to 0.9333 and from 0.427 to 0.8819 per locus, respectively. Cross-species amplifications of all 16 primer pairs were tested in four other species of catfish including Clarias gariepinus, Pangasius hypophthalmus, Pangasius larnaudii and Pangasianodon gigas. Eleven loci were found to amplify in other species, with the number of polymorphic loci ranging from one in P. larnaudii to nine in C. gariepinus.

  7. Development and characterization of microsatellite markers of the eastern keelback mullet (Liza affinis).

    Science.gov (United States)

    Liu, L; Gao, T X; Han, Z Q; Li, C H; Sun, D R; Song, N

    2016-06-17

    Twenty-four polymorphic microsatellite loci were isolated and characterized for Liza affinis using a (GT)13-enriched genomic library. The number of alleles per locus ranged from 3 to 9, with a mean number of 6.250. The observed and expected heterozygosities ranged from 0.417 to 1.000 and from 0.550 to 0.861, with an average of 0.859 and 0.779, respectively. Deviation from Hardy-Weinberg proportions was detected at three loci. Evidence of null alleles was found at two loci. These markers will be useful in further studies investigating the genetic variation and population structure of this species, and may provide insights into the maintenance and efficient management of eastern keelback mullet resources.

  8. PERMANENT GENETIC RESOURCES: Eighteen new polymorphic microsatellite markers for the endangered Florida manatee, Trichechus manatus latirostris.

    Science.gov (United States)

    Tringali, Michael D; Seyoum, Seifu; Carney, Susan L; Davis, Michelle C; Rodriguez-Lopez, Marta A; Reynolds Iii, John E; Haubold, Elsa

    2008-03-01

    Here we describe 18 polymorphic microsatellite loci for Trichechus manatus latirostris (Florida manatee), isolated using a polymerase chain reaction-based technique. The number of alleles at each locus ranged from two to four (mean = 2.5) in specimens from southwest (n = 58) and northeast (n = 58) Florida. Expected and observed heterozygosities ranged from 0.11 to 0.67 (mean = 0.35) and from 0.02 to 0.78 (mean = 0.34), respectively. Departures from Hardy-Weinberg equilibrium occurred at two loci. There was no evidence of genotypic disequilibrium for any pair of loci. For individual identification, mean random-mating and θ-corrected match probabilities were 9.36 × 10(-7) and 1.95 × 10(-6) , respectively. © 2007 The Authors.

  9. Microsatellite DNA polymorphisms and the relation with body weight in sea cucumber Apostichopus japonicus

    Institute of Scientific and Technical Information of China (English)

    WANG Xiuli; SHAN Xue; QIU Xuemei; MENG Xiangying; CHANG Yaqing

    2009-01-01

    The relationship between microsatellite polymorphism and body weight of captive bred Chinese sea cucumber Apostichopus japonicus was investigated in two local populations in Dalian.Among ten loci discovered, nine show changes except for A J07 loci. Seven loci were found highly polymorphic in both populations. For each locus in two populations, the average number of alleles is 6.428 6 and 6.285 7, the average observed heterozygosity at 0.225 7 and 0.245 9, the expected heterozygosity at 0.776 8 and 0.748 8, the polymorphism information content (PIC) at 0.709 2 and 0.674 6, respectively. Further analysis show significant correlation between A. japonicus body weight and occurrence markers AJ02 and AJ04. The findings of the relation may be helpful for molecular breeding,as well as the marker-assisted selection of sea cucumbers.

  10. Sinanodonta woodiana (Mollusca: Bivalvia: Unionidae: Isolation and Characterization of the First Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Elena Iulia Iorgu

    2011-08-01

    Full Text Available Sinanodonta woodiana (Lea, 1834 is a large Unionid species with a real invasion success. It colonized Europe, Central America, the Indonesian Islands and recently North America. The species life cycle involves a larval parasitic stage on freshwater fish species which contributes to the spread of the mussel. In this paper we describe, for the first time, eight polymorphic microsatellite loci for the species Sinanodonta woodiana. The genetic screening of individuals confirmed that all loci were highly polymorphic. The number of alleles per locus ranged from 7 to 14 and the observed heterozygosity ranged from 0.650 to 0.950. These loci should prove useful to study the species population genetics which could help to infer important aspects of the invasion process.

  11. Characterization of microsatellites in wild and sweet cherry (Prunus avium L.)--markers for individual identification and reproductive processes.

    Science.gov (United States)

    Schueler, Silvio; Tusch, Alexandra; Schuster, Mirko; Ziegenhagen, Birgit

    2003-02-01

    Nuclear microsatellites were characterized in Prunus avium and validated as markers for individual and cultivar identification, as well as for studies of pollen- and seed-mediated gene flow. We used 20 primer pairs from a simple sequence repeat (SSR) library of Prunus persica and identified 7 loci harboring polymorphic microsatellite sequences in P. avium. In a natural population of 75 wild cherry trees, the number of alleles per locus ranged from 4 to 9 and expected heterozygosity from 0.39 to 0.77. The variability of the SSR markers allowed an unambiguous identification of individual trees and potential root suckers. Additionally, we analyzed 13 sweet cherry cultivars and differentiated 12 of them. An exclusion probability of 0.984 was calculated, which indicates that the seven loci are suitable markers for paternity analysis. The woody endocarp was successfully used for resolution of all microsatellite loci and exhibited the same multilocus genotype as the mother tree, as shown in a single seed progeny. Hence, SSR fingerprinting of the purely maternal endocarp was also successful in this Prunus species, allowing the identification of the mother tree of the dispersed seeds. The linkage of microsatellite loci with PCR-amplified alleles of the self-incompatibility locus was tested in two full-sib families of sweet cherry cultivars. From low recombination frequencies, we inferred that two loci are linked with the S locus. The present study provides markers that will significantly facilitate studies of spatial genetic variation and gene flow in wild cherry, as well as breeding programs in sweet cherry.

  12. Genetic Diversity of Bali Cattle Based on Microsatellite Marker in Indonesian Breeding Centre

    Directory of Open Access Journals (Sweden)

    W. A. Septian

    2015-04-01

    Full Text Available Genetics characterization in livestock based on microsatellite has been widely implemented including for Bali cattle in three different breeding centres in Indonesia. This study aimed to determine diversity of Bali cattle microsatellites in three breeding centers namely BPTU Bali cattle in Bali, BPT-HMT Serading Sumbawa in West Nusa Tenggara, and Village Breeding Center in South Sulawesi. The number of animals used in this study was 95 head of cattle consisted of 32 heads from BPTU Bali Province, 32 heads from BPT-HMT Serading Sumbawa, and 31 heads from Village Barru Breeding Center Barru distric. Microsatellite loci used to determine the diversity was the locus SPS115, INRA037, MM12, and ETH185 based on flourescently labeled fragment method. Data analysis of microsatellite in Bali cattle at three different locations was performed by using POPGEN 1.2, Cervus, and POPTREE2 programs. The results showed that microsatellite diversity in Bali cattle detected 32 alleles from three different locations, and there were specific alleles at each location. Average values of observed heterozygosity (Ho and expected heterozygosity (He were 0.418 and 0.604 respectively, while the average value of polymorphism informative content (PIC was 0.579. The Hardy-Weinberg equilibrium in general suggested that the loci used in the Bali cattle in three populations were in equilibrium, except INRA037 and ETH185. The genetic diversity between populations of Bali cattle was 0.033 (3%, while the inbreeding coefficient index in all populations was 0.296 (29.6 %. Bali cattle phylogeny tree with three populations showed that the populations of Bali cattle in BPTU Bali and VBC Barru had close genetic distance compared to the population of Bali cattle in BPT-HMT Serading Sumbawa. The results of this study provide information that the characteristics of Bali cattle breeding centers in three locations are different, so we need a directed breeding program in each population.

  13. Twelve tips for peer observation of teaching.

    Science.gov (United States)

    Siddiqui, Zarrin Seema; Jonas-Dwyer, Diana; Carr, Sandra E

    2007-05-01

    This paper outlines twelve tips for undertaking peer observation of teaching in medical education, using the peer review model and the experiences of the authors. An accurate understanding of teaching effectiveness is required by individuals, medical schools, and universities to evaluate the learning environment and to substantiate academic and institutional performance. Peer Observation of Teaching is one tool that provides rich, qualitative evidence for teachers, quite different from closed-ended student evaluations. When Peer Observation of Teaching is incorporated into university practice and culture, and is conducted in a mutually respectful and supportive way, it has the potential to facilitate reflective change and growth for teachers.

  14. Amplification of rainbow trout microsatellites in Brachymystax lenok.

    Science.gov (United States)

    Jia, Z Y; Zhang, Y Y; Shi, L Y; Bai, Q L; Jin, S B; Mou, Z B

    2008-11-01

    Brachymystax lenok is a cold freshwater fish accustomed to inhabit relatively high concentration of dissolved oxygen and clean upper streams. Here we present 13 polymorphic microsatellite primer pairs from rainbow trout to amplify in 32 B. lenok individuals from Ussuri River of China. The number of alleles ranged from two to seven with an average of 3.9 per locus. Observed heterozygosity ranged from 0.0625 to 0.9677. One locus showed significant deviation from Hardy-Weinberg equilibrium. These 13 loci will provide a good basis for investigation of B. lenok population structure and genetic diversity in different distribution region. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

  15. What is a microsatellite: a computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats.

    Science.gov (United States)

    Kelkar, Yogeshwar D; Strubczewski, Noelle; Hile, Suzanne E; Chiaromonte, Francesca; Eckert, Kristin A; Makova, Kateryna D

    2010-01-01

    Microsatellites are abundant in eukaryotic genomes and have high rates of strand slippage-induced repeat number alterations. They are popular genetic markers, and their mutations are associated with numerous neurological diseases. However, the minimal number of repeats required to constitute a microsatellite has been debated, and a definition of a microsatellite that considers its mutational behavior has been lacking. To define a microsatellite, we investigated slippage dynamics for a range of repeat sizes, utilizing two approaches. Computationally, we assessed length polymorphism at repeat loci in ten ENCODE regions resequenced in four human populations, assuming that the occurrence of polymorphism reflects strand slippage rates. Experimentally, we determined the in vitro DNA polymerase-mediated strand slippage error rates as a function of repeat number. In both approaches, we compared strand slippage rates at tandem repeats with the background slippage rates. We observed two distinct modes of mutational behavior. At small repeat numbers, slippage rates were low and indistinguishable from background measurements. A marked transition in mutability was observed as the repeat array lengthened, such that slippage rates at large repeat numbers were significantly higher than the background rates. For both mononucleotide and dinucleotide microsatellites studied, the transition length corresponded to a similar number of nucleotides (approximately 10). Thus, microsatellite threshold is determined not by the presence/absence of strand slippage at repeats but by an abrupt alteration in slippage rates relative to background. These findings have implications for understanding microsatellite mutagenesis, standardization of genome-wide microsatellite analyses, and predicting polymorphism levels of individual microsatellite loci.

  16. Quantitative trait loci (QTLs) analysis of palm oil fatty acid composition in an interspecific pseudo-backcross from Elaeis oleifera (HBK) Cortés and oil palm (Elaeis guineensis Jacq.)

    OpenAIRE

    Montoya, Carmenza; Lopes, Ricardo; Flori, Albert; Cros, David; Cuellar, Teresa; Summo, Maryline; Espeout, Sandra; Rivallan, Ronan; Risterucci, Ange-Marie; Bittencourt, Daniela; Zambrano, Jorge R.; Alarcon G, Wilmar H.; Villeneuve, Pierre; Pina, Michel; Nouy, Bruno

    2013-01-01

    We chose an Elaeis interspecific pseudo-backcross of first generation (E. oleifera x E. guineensis) x E. guineensis to identify quantitative trait loci (QTLs) for fatty acid composition of palm oil. A dense microsatellite linkage map of 362 loci spanned 1.485 cM, representing the 16 pairs of homologous chromosomes in the Elaeis genus from which we traced segregating alleles from both E. oleifera and E. guineensis grandparents. The relative linear orders of mapped loci suggested the probable a...

  17. Origin, evolution and genome distribution of microsatellites

    Directory of Open Access Journals (Sweden)

    Eder Jorge Oliveira

    2006-01-01

    Full Text Available Microsatellites, or simple sequence repeats (SSRs, have been the most widely applied class of molecular markers used in genetic studies, with applications in many fields of genetics including genetic conservation, population genetics, molecular breeding, and paternity testing. This range of applications is due to the fact that microsatellite markers are co-dominant and multi-allelic, are highly reproducible, have high-resolution and are based on the polymerase chain reaction (PCR. When first introduced, the development of microsatellite markers was expensive but now new and efficient methods of repetitive sequence isolation have been reported, which have led to reduced costs and microsatellite-technology has been increasingly applied to several species, including non-model organisms. The advent of microsatellite markers revolutionized the use of molecular markers but the development of biometric methods for analyzing microsatellite data has not accompanied the progress in the application of these markers, with more effort being need to obtain information on the evolution of the repetitive sequences, which constitute microsatellites in order to formulate models that fit the characteristics of such markers. Our review describes the genetic nature of microsatellites, the mechanisms and models of mutation that control their evolution and aspects related to their genesis, distribution and transferability between taxa. The implications of the use of microsatellites as a tool for estimating genetic parameters are also discussed.

  18. FullSSR: Microsatellite Finder and Primer Designer

    Directory of Open Access Journals (Sweden)

    Sebastián Metz

    2016-01-01

    Full Text Available Microsatellites are genomic sequences comprised of tandem repeats of short nucleotide motifs widely used as molecular markers in population genetics. FullSSR is a new bioinformatic tool for microsatellite (SSR loci detection and primer design using genomic data from NGS assay. The software was tested with 2000 sequences of Oryza sativa shotgun sequencing project from the National Center of Biotechnology Information Trace Archive and with partial genome sequencing with ROCHE 454® from Caiman latirostris, Salvator merianae, Aegla platensis, and Zilchiopsis collastinensis. FullSSR performance was compared against other similar SSR search programs. The results of the use of this kind of approach depend on the parameters set by the user. In addition, results can be affected by the analyzed sequences because of differences among the genomes. FullSSR simplifies the detection of SSRs and primer design on a big data set. The command line interface of FullSSR was intended to be used as part of genomic analysis tools pipeline; however, it can be used as a stand-alone program because the results are easily interpreted for a nonexpert user.

  19. Genetic structure of Balearic honeybee populations based on microsatellite polymorphism

    Directory of Open Access Journals (Sweden)

    Moritz Robin FA

    2003-05-01

    Full Text Available Abstract The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca and Pitiusas (Ibiza and Formentera, which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees.

  20. FullSSR: Microsatellite Finder and Primer Designer

    Science.gov (United States)

    Metz, Sebastián; Cabrera, Juan Manuel; Rueda, Eva; Giri, Federico; Amavet, Patricia

    2016-01-01

    Microsatellites are genomic sequences comprised of tandem repeats of short nucleotide motifs widely used as molecular markers in population genetics. FullSSR is a new bioinformatic tool for microsatellite (SSR) loci detection and primer design using genomic data from NGS assay. The software was tested with 2000 sequences of Oryza sativa shotgun sequencing project from the National Center of Biotechnology Information Trace Archive and with partial genome sequencing with ROCHE 454® from Caiman latirostris, Salvator merianae, Aegla platensis, and Zilchiopsis collastinensis. FullSSR performance was compared against other similar SSR search programs. The results of the use of this kind of approach depend on the parameters set by the user. In addition, results can be affected by the analyzed sequences because of differences among the genomes. FullSSR simplifies the detection of SSRs and primer design on a big data set. The command line interface of FullSSR was intended to be used as part of genomic analysis tools pipeline; however, it can be used as a stand-alone program because the results are easily interpreted for a nonexpert user. PMID:27366148

  1. Study of microsatellite instability in epithelial ovarian tumors%上皮性卵巢癌中微卫星不稳定的研究

    Institute of Scientific and Technical Information of China (English)

    卢媛; 刘惜时; 王跃祥; 宋后燕; Nanbert ZHONG

    2006-01-01

    Objective: To evaluate the frequency of MSI in epithelial ovarian tumors and its relationship with clinicopathologic features. Methods: Ninety fresh specimens of epithelial ovarian tumors, including 74 primary and 16 secondary tumors, were collected. Microsatellite analysis was carried out using 5 mono- and dinucleotide markers from the National Cancer Institute Consensus Panel by fluorescence-labeled polymerase chain reaction. Results: Of 90 epithelial ovarian tumors analyzed, 18 demonstrated a high level of microsatellite instability (MSI-H), 30 demonstrated a low level of microsatellite instability (MSI-L), and the remaining 42 exhibited microsatellite stability (MSS). Frequency of microsatellite instability (MSI) at loci BAT-25 was higher than that at any other loci. No correlation was found between MSI level and patient age, tumor type, tumor differentiation (P>0.05). But the microsatellite instability-high phenotype correlates with clinical stage.It tended to occur more frequently in early-stage tumors (P=0.03). Conclusion: The frequent MSI in epithelial ovarian tumors suggests that it is an early event to involve in the development of epithelial ovarian tumors.

  2. Nuclear microsatellite markers for the date palm (Phoenix dactylifera L.): characterization and utility across the genus Phoenix and in other palm genera.

    NARCIS (Netherlands)

    Billotte, N.; Marseillac, P.; Brottier, P.; Noyer, J.L.; Jacquemoud, J.P.; Moreau, C.; Couvreur, T.L.P.; Chavallier, M.H.; Pintaud, J.C.; Risterucci, A.M.

    2004-01-01

    A (GA)n microsatellite-enriched library was constructed and 16 nuclear simple sequence repeat (SSR) loci were characterized in Phoenix dactylifera. Across-taxa amplification and genotyping tests showed the utility of most SSR markers in 11 other Phoenix species and the transferability of some of the

  3. Searching for a stock structure in Sardina pilchardus from the Adriatic and Ionian seas using a microsatellite DNA-based approach

    DEFF Research Database (Denmark)

    Ruggeri, Paolo; Splendiani, Andrea; Bonanomi, Sara;

    2013-01-01

    In the present study the genetic variability of European sardine from Adriatic and Ionian seas was investigated in order to detect the occurrence of genetic structure within and between these basins. In several samples the analysis of genetic variability at eight microsatellite loci showed a numb...

  4. New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk

    NARCIS (Netherlands)

    Lu, Yingchang; Day, Felix R; Gustafsson, Stefan; Buchkovich, Martin L; Na, Jianbo; Bataille, Veronique; Cousminer, Diana L; Dastani, Zari; Drong, Alexander W; Esko, Tõnu; Evans, David M; Falchi, Mario; Feitosa, Mary F; Ferreira, Teresa; Hedman, Åsa K; Haring, Robin; Hysi, Pirro G; Iles, Mark M; Justice, Anne E; Kanoni, Stavroula; Lagou, Vasiliki; Li, Rui; Li, Xin; Locke, Adam; Lu, Chen; Mägi, Reedik; Perry, John R B; Pers, Tune H; Qi, Qibin; Sanna, Marianna; Schmidt, Ellen M; Scott, William R; Shungin, Dmitry; Teumer, Alexander; Vinkhuyzen, Anna A E; Walker, Ryan W; Westra, Harm-Jan; Zhang, Mingfeng; Zhang, Weihua; Zhao, Jing Hua; Zhu, Zhihong; Afzal, Uzma; Ahluwalia, Tarunveer Singh; Bakker, Stephan J L; Bellis, Claire; Bonnefond, Amélie; Borodulin, Katja; Buchman, Aron S; Cederholm, Tommy; Choh, Audrey C; Choi, Hyung Jin; Curran, Joanne E; de Groot, Lisette C P G M; De Jager, Philip L; Dhonukshe-Rutten, Rosalie A M; Enneman, Anke W; Eury, Elodie; Evans, Daniel S; Forsen, Tom; Friedrich, Nele; Fumeron, Frédéric; Garcia, Melissa E; Gärtner, Simone; Han, Bok-Ghee; Havulinna, Aki S; Hayward, Caroline; Hernandez, Dena; Hillege, Hans; Ittermann, Till; Kent, Jack W; Kolcic, Ivana; Laatikainen, Tiina; Lahti, Jari; Mateo Leach, Irene; Lee, Christine G; Lee, Jong-Young; Liu, Tian; Liu, Youfang; Lobbens, Stéphane; Loh, Marie; Lyytikäinen, Leo-Pekka; Medina-Gomez, Carolina; Michaëlsson, Karl; Nalls, Mike A; Nielson, Carrie M; Oozageer, Laticia; Pascoe, Laura; Paternoster, Lavinia; Polašek, Ozren; Ripatti, Samuli; Sarzynski, Mark A; Shin, Chan Soo; Narančić, Nina Smolej; Spira, Dominik; Srikanth, Priya; Steinhagen-Thiessen, Elisabeth; Sung, Yun Ju; Swart, Karin M A; Taittonen, Leena; Tanaka, Toshiko; Tikkanen, Emmi; van der Velde, Nathalie; van Schoor, Natasja M; Verweij, Niek; Wright, Alan F; Yu, Lei; Zmuda, Joseph M; Eklund, Niina; Forrester, Terrence; Grarup, Niels; Jackson, Anne U; Kristiansson, Kati; Kuulasmaa, Teemu; Kuusisto, Johanna; Lichtner, Peter; Luan, Jian'an; Mahajan, Anubha; Männistö, Satu; Palmer, Cameron D; Ried, Janina S; Scott, Robert A; Stancáková, Alena; Wagner, Peter J; Demirkan, Ayse; Döring, Angela; Gudnason, Vilmundur; Kiel, Douglas P; Kühnel, Brigitte; Mangino, Massimo; Mcknight, Barbara; Menni, Cristina; O'Connell, Jeffrey R; Oostra, Ben A; Shuldiner, Alan R; Song, Kijoung; Vandenput, Liesbeth; van Duijn, Cornelia M; Vollenweider, Peter; White, Charles C; Boehnke, Michael; Boettcher, Yvonne; Cooper, Richard S; Forouhi, Nita G; Gieger, Christian; Grallert, Harald; Hingorani, Aroon; Jørgensen, Torben; Jousilahti, Pekka; Kivimaki, Mika; Kumari, Meena; Laakso, Markku; Langenberg, Claudia; Linneberg, Allan; Luke, Amy; Mckenzie, Colin A; Palotie, Aarno; Pedersen, Oluf; Peters, Annette; Strauch, Konstantin; Tayo, Bamidele O; Wareham, Nicholas J; Bennett, David A; Bertram, Lars; Blangero, John; Blüher, Matthias; Bouchard, Claude; Campbell, Harry; Cho, Nam H; Cummings, Steven R; Czerwinski, Stefan A; Demuth, Ilja; Eckardt, Rahel; Eriksson, Johan G; Ferrucci, Luigi; Franco, Oscar H; Froguel, Philippe; Gansevoort, Ron T; Hansen, Torben; Harris, Tamara B; Hastie, Nicholas; Heliövaara, Markku; Hofman, Albert; Jordan, Joanne M; Jula, Antti; Kähönen, Mika; Kajantie, Eero; Knekt, Paul B; Koskinen, Seppo; Kovacs, Peter; Lehtimäki, Terho; Lind, Lars; Liu, Yongmei; Orwoll, Eric S; Osmond, Clive; Perola, Markus; Pérusse, Louis; Raitakari, Olli T; Rankinen, Tuomo; Rao, D C; Rice, Treva K; Rivadeneira, Fernando; Rudan, Igor; Salomaa, Veikko; Sørensen, Thorkild I A; Stumvoll, Michael; Tönjes, Anke; Towne, Bradford; Tranah, Gregory J; Tremblay, Angelo; Uitterlinden, André G; van der Harst, Pim; Vartiainen, Erkki; Viikari, Jorma S; Vitart, Veronique; Vohl, Marie-Claude; Völzke, Henry; Walker, Mark; Wallaschofski, Henri; Wild, Sarah; Wilson, James F; Yengo, Loïc; Bishop, D Timothy; Borecki, Ingrid B; Chambers, John C; Cupples, L Adrienne; Dehghan, Abbas; Deloukas, Panos; Fatemifar, Ghazaleh; Fox, Caroline; Furey, Terrence S; Franke, Lude; Han, Jiali; Hunter, David J; Karjalainen, Juha; Karpe, Fredrik; Kaplan, Robert C; Kooner, Jaspal S; McCarthy, Mark I; Murabito, Joanne M; Morris, Andrew P; Bishop, Julia A N; North, Kari E; Ohlsson, Claes; Ong, Ken K; Prokopenko, Inga; Richards, J Brent; Schadt, Eric E; Spector, Tim D; Widén, Elisabeth; Willer, Cristen J; Yang, Jian; Ingelsson, Erik; Mohlke, Karen L; Hirschhorn, Joel N; Pospisilik, John Andrew; Zillikens, M Carola; Lindgren, Cecilia; Kilpeläinen, Tuomas Oskari; Loos, Ruth J F

    2016-01-01

    To increase our understanding of the genetic basis of adiposity and its links to cardiometabolic disease risk, we conducted a genome-wide association meta-analysis of body fat percentage (BF%) in up to 100,716 individuals. Twelve loci reached genome-wide significance (P<5 × 10(-8)), of which eight w

  5. New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk

    NARCIS (Netherlands)

    Lu, Yingchang; Day, Felix R; Gustafsson, Stefan; Buchkovich, Martin L; Na, Jianbo; Bataille, Veronique; Cousminer, Diana L; Dastani, Zari; Drong, Alexander W; Esko, Tõnu; Evans, David M; Falchi, Mario; Feitosa, Mary F; Ferreira, Teresa; Hedman, Åsa K; Haring, Robin; Hysi, Pirro G; Iles, Mark M; Justice, Anne E; Kanoni, Stavroula; Lagou, Vasiliki; Li, Rui; Li, Xin; Locke, Adam; Lu, Chen; Mägi, Reedik; Perry, John R B; Pers, Tune H; Qi, Qibin; Sanna, Marianna; Schmidt, Ellen M; Scott, William R; Shungin, Dmitry; Teumer, Alexander; Vinkhuyzen, Anna A E; Walker, Ryan W; Westra, Harm-Jan; Zhang, Mingfeng; Zhang, Weihua; Zhao, Jing Hua; Zhu, Zhihong; Afzal, Uzma; Ahluwalia, Tarunveer Singh; Bakker, Stephan J L; Bellis, Claire; Bonnefond, Amélie; Borodulin, Katja; Buchman, Aron S; Cederholm, Tommy; Choh, Audrey C; Choi, Hyung Jin; Curran, Joanne E; de Groot, Lisette C P G M; De Jager, Philip L; Dhonukshe-Rutten, Rosalie A M; Enneman, Anke W; Eury, Elodie; Evans, Daniel S; Forsen, Tom; Friedrich, Nele; Fumeron, Frédéric; Garcia, Melissa E; Gärtner, Simone; Han, Bok-Ghee; Havulinna, Aki S; Hayward, Caroline; Hernandez, Dena; Hillege, Hans; Ittermann, Till; Kent, Jack W; Kolcic, Ivana; Laatikainen, Tiina; Lahti, Jari; Mateo Leach, Irene; Lee, Christine G; Lee, Jong-Young; Liu, Tian; Liu, Youfang; Lobbens, Stéphane; Loh, Marie; Lyytikäinen, Leo-Pekka; Medina-Gomez, Carolina; Michaëlsson, Karl; Nalls, Mike A; Nielson, Carrie M; Oozageer, Laticia; Pascoe, Laura; Paternoster, Lavinia; Polašek, Ozren; Ripatti, Samuli; Sarzynski, Mark A; Shin, Chan Soo; Narančić, Nina Smolej; Spira, Dominik; Srikanth, Priya; Steinhagen-Thiessen, Elisabeth; Sung, Yun Ju; Swart, Karin M A; Taittonen, Leena; Tanaka, Toshiko; Tikkanen, Emmi; van der Velde, Nathalie; van Schoor, Natasja M; Verweij, Niek; Wright, Alan F; Yu, Lei; Zmuda, Joseph M; Eklund, Niina; Forrester, Terrence; Grarup, Niels; Jackson, Anne U; Kristiansson, Kati; Kuulasmaa, Teemu; Kuusisto, Johanna; Lichtner, Peter; Luan, Jian'an; Mahajan, Anubha; Männistö, Satu; Palmer, Cameron D; Ried, Janina S; Scott, Robert A; Stancáková, Alena; Wagner, Peter J; Demirkan, Ayse; Döring, Angela; Gudnason, Vilmundur; Kiel, Douglas P; Kühnel, Brigitte; Mangino, Massimo; Mcknight, Barbara; Menni, Cristina; O'Connell, Jeffrey R; Oostra, Ben A; Shuldiner, Alan R; Song, Kijoung; Vandenput, Liesbeth; van Duijn, Cornelia M; Vollenweider, Peter; White, Charles C; Boehnke, Michael; Boettcher, Yvonne; Cooper, Richard S; Forouhi, Nita G; Gieger, Christian; Grallert, Harald; Hingorani, Aroon; Jørgensen, Torben; Jousilahti, Pekka; Kivimaki, Mika; Kumari, Meena; Laakso, Markku; Langenberg, Claudia; Linneberg, Allan; Luke, Amy; Mckenzie, Colin A; Palotie, Aarno; Pedersen, Oluf; Peters, Annette; Strauch, Konstantin; Tayo, Bamidele O; Wareham, Nicholas J; Bennett, David A; Bertram, Lars; Blangero, John; Blüher, Matthias; Bouchard, Claude; Campbell, Harry; Cho, Nam H; Cummings, Steven R; Czerwinski, Stefan A; Demuth, Ilja; Eckardt, Rahel; Eriksson, Johan G; Ferrucci, Luigi; Franco, Oscar H; Froguel, Philippe; Gansevoort, Ron T; Hansen, Torben; Harris, Tamara B; Hastie, Nicholas; Heliövaara, Markku; Hofman, Albert; Jordan, Joanne M; Jula, Antti; Kähönen, Mika; Kajantie, Eero; Knekt, Paul B; Koskinen, Seppo; Kovacs, Peter; Lehtimäki, Terho; Lind, Lars; Liu, Yongmei; Orwoll, Eric S; Osmond, Clive; Perola, Markus; Pérusse, Louis; Raitakari, Olli T; Rankinen, Tuomo; Rao, D C; Rice, Treva K; Rivadeneira, Fernando; Rudan, Igor; Salomaa, Veikko; Sørensen, Thorkild I A; Stumvoll, Michael; Tönjes, Anke; Towne, Bradford; Tranah, Gregory J; Tremblay, Angelo; Uitterlinden, André G; van der Harst, Pim; Vartiainen, Erkki; Viikari, Jorma S; Vitart, Veronique; Vohl, Marie-Claude; Völzke, Henry; Walker, Mark; Wallaschofski, Henri; Wild, Sarah; Wilson, James F; Yengo, Loïc; Bishop, D Timothy; Borecki, Ingrid B; Chambers, John C; Cupples, L Adrienne; Dehghan, Abbas; Deloukas, Panos; Fatemifar, Ghazaleh; Fox, Caroline; Furey, Terrence S; Franke, Lude; Han, Jiali; Hunter, David J; Karjalainen, Juha; Karpe, Fredrik; Kaplan, Robert C; Kooner, Jaspal S; McCarthy, Mark I; Murabito, Joanne M; Morris, Andrew P; Bishop, Julia A N; North, Kari E; Ohlsson, Claes; Ong, Ken K; Prokopenko, Inga; Richards, J Brent; Schadt, Eric E; Spector, Tim D; Widén, Elisabeth; Willer, Cristen J; Yang, Jian; Ingelsson, Erik; Mohlke, Karen L; Hirschhorn, Joel N; Pospisilik, John Andrew; Zillikens, M Carola; Lindgren, Cecilia; Kilpeläinen, Tuomas Oskari; Loos, Ruth J F

    2016-01-01

    To increase our understanding of the genetic basis of adiposity and its links to cardiometabolic disease risk, we conducted a genome-wide association meta-analysis of body fat percentage (BF%) in up to 100,716 individuals. Twelve loci reached genome-wide significance (P<5 × 10(-8)), of which eight w

  6. New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk

    NARCIS (Netherlands)

    Y. Lu (Yingchang); F.R. Day (Felix); S. Gustafsson (Stefan); M.L. Buchkovich (Martin); Na, J. (Jianbo); V. Bataille (Veronique); D.L. Cousminer (Diana); Z. Dastani (Zari); A. Drong (Alexander); T. Esko (Tõnu); D.M. Evans (David); M. Falchi (Mario); M.F. Feitosa (Mary Furlan); T. Ferreira (Teresa); A.K. Hedman (Asa); R. Haring (Robin); P.G. Hysi (Pirro); M.M. Iles (Mark M.); A.E. Justice (Anne); S. Kanoni (Stavroula); V. Lagou (Vasiliki); R. Li (Rui); X. Li (Xin); A. Locke (Adam); C. Lu (Chao); R. Mägi (Reedik); J.R.B. Perry (John); T.H. Pers (Tune); Q. Qi; Sanna, M. (Marianna); E.M. Schmidt (Ellen); W.R. Scott (William R.); D. Shungin (Dmitry); A. Teumer (Alexander); A.A.E. Vinkhuyzen (Anna A.); Walker, R.W. (Ryan W.); H.J. Westra (Harm-Jan); M. Zhang (Mingfeng); W. Zhang (Weihua); J.H. Zhao; Z. Zhu; U. Afzal (Uzma); T.S. Ahluwalia (Tarunveer Singh); S.J.L. Bakker (Stephan); C. Bellis (Claire); A. Bonnefond (Amélie); K. Borodulin (Katja); Buchman, A.S. (Aron S.); T. Cederholm (Tommy); A.C. Choh (Audrey); Choi, H.J. (Hyung Jin); J.E. Curran (Joanne); L.C.P.G.M. de Groot (Lisette); P.L. de Jager (Philip); R.A.M. Dhonukshe-Rutten (Rosalie); A.W. Enneman (Anke); E. Eury (Elodie); D.S. Evans (Daniel); T. Forsen (Tom); N. Friedrich (Nele); Fumeron, F. (Frédéric); M. Garcia (Melissa); Gärtner, S. (Simone); B.-G. Han; A.S. Havulinna (Aki); C. Hayward (Caroline); D.G. Hernandez (Dena); H.L. Hillege (Hans); T. Ittermann (Till); J.W. Kent (Jack W.); I. Kolcic (Ivana); T. Laatikainen (Tiina); J. Lahti (Jari); I.M. Leach (Irene Mateo); Lee, C.G. (Christine G.); J.-Y. Lee (Jong-Young); T. Liu (Tian); Liu, Y. (Youfang); S. Lobbens (Stéphane); Loh, M. (Marie); L.-P. Lyytikäinen (Leo-Pekka); Medina-Gomez, C. (Carolina); K. Michaëlsson; M.A. Nalls (Michael); C. Nielson (Carrie); L. Oozageer (Laticia); L. Pascoe (Laura); L. Paternoster (Lavinia); O. Polasek (Ozren); S. Ripatti (Samuli); M.A. Sarzynski (Mark A.); Shin, C.S. (Chan Soo); Naranäiä, N.S. (Nina Smolej); Spira, D. (Dominik); P. Srikanth (Priya); Steinhagen-Thiessen, E. (Elisabeth); Sung, Y.J. (Yun Ju); K.M.A. Swart (Karin); Taittonen, L. (Leena); T. Tanaka (Toshiko); E. Tikkanen (Emmi); N. van der Velde (Nathalie); N.M. van Schoor (Natasja); N. Verweij (Niek); A.F. Wright (Alan); L. Yu (Lei); J. Zmuda (Joseph); N. Eklund (Niina); T. Forrester (Terrence); N. Grarup (Niels); A.U. Jackson (Anne); K. Kristiansson (Kati); T. Kuulasmaa (Teemu); J. Kuusisto (Johanna); P. Lichtner (Peter); J. Luan (Jian'An); A. Mahajan (Anubha); S. Männistö (Satu); C. Palmer (Cameron); J.S. Ried (Janina); R.A. Scott (Robert); A. Stancáková (Alena); P.J. Wagner (Peter); A. Demirkan (Ayşe); A. Döring (Angela); V. Gudnason (Vilmundur); D.P. Kiel (Douglas P.); B. Kuhnel (Brigitte); M. Mangino (Massimo); B. McKnight (Barbara); C. Menni (Cristina); O'Connell, J.R. (Jeffrey R.); B.A. Oostra (Ben); A.R. Shuldiner (Alan); K. Song (Kijoung); L. Vandenput (Liesbeth); C.M. van Duijn (Cock); P. Vollenweider (Peter); C.C. White (Charles); M. Boehnke (Michael); Boettcher, Y. (Yvonne); Cooper, R.S. (Richard S.); N.G. Forouhi (Nita); C. Gieger (Christian); H. Grallert (Harald); A. Hingorani (Aroon); T. Jorgensen (Torben); P. Jousilahti (Pekka); M. Kivimaki (Mika); M. Kumari (Meena); M. Laakso (Markku); C. Langenberg (Claudia); A. Linneberg (Allan); Luke, A. (Amy); C.A. McKenzie (Colin); A. Palotie (Aarno); O. Pedersen (Oluf); A. Peters (Annette); K. Strauch (Konstantin); B. Tayo (Bamidele); N.J. Wareham (Nick); D.A. Bennett (David A.); L. Bertram (Lars); J. Blangero (John); M. Blüher (Matthias); C. Bouchard (Claude); H. Campbell (Harry); Cho, N.H. (Nam H.); S.R. Cummings (Steven R.); S.A. Czerwinski (Stefan); I. Demuth (Ilja); Eckardt, R. (Rahel); K. Hagen (Knut); L. Ferrucci (Luigi); O.H. Franco (Oscar); P. Froguel (Philippe); R.T. Gansevoort (Ron); T. Hansen (T.); T.B. Harris (Tamara); N. Hastie (Nick); M. Heliovaara (Markku); Hofman, A. (Albert); Jordan, J.M. (Joanne M.); A. Jula (Antti); M. Kähönen (Mika); E. Kajantie (Eero); P. Knekt; Koskinen, S. (Seppo); P. Kovacs (Peter); T. Lehtimäki (Terho); W.H.L. Kao (Wen); Y. Liu (Yongmei); E.S. Orwoll (Eric); C. Osmond (Clive); M. Perola (Markus); L. Perusse (Louis); Raitakari, O.T. (Olli T.); T. Rankinen (Tuomo); Rao, D.C.; Rice, T.K. (Treva K.); F. Rivadeneira Ramirez (Fernando); I. Rudan (Igor); V. Salomaa (Veikko); T.I.A. Sørensen (Thorkild); M. Stumvoll (Michael); A. Tönjes (Anke); B. Towne (Bradford); G.J. Tranah (Gregory); Tremblay, A. (Angelo); A.G. Uitterlinden (André); P. van der Harst (Pim); Vartiainen, E. (Erkki); J. Viikari (Jorma); Vitart, V. (Veronique); M.-C. Vohl (Marie-Claude); H. Völzke (Henry); Walker, M. (Mark); H. Wallaschofski (Henri); S.H. Wild (Sarah); J.F. Wilson (James F.); L. Yengo (Loic); D.T. Bishop (David Timothy); I.B. Borecki (Ingrid); J.C. Chambers (John C.); L.A. Cupples (Adrienne); A. Dehghan (Abbas); P. Deloukas (Panagiotis); Fatemifar, G. (Ghazaleh); C.S. Fox (Caroline); Furey, T.S. (Terrence S.); L. Franke (Lude); J. Han; D. Hunter (David); J. Karjalainen (Juha); F. Karpe (Fredrik); R.C. Kaplan (Robert); J.S. Kooner (Jaspal S.); M.I. McCarthy (Mark); J. Murabito (Joanne); A.P. Morris (Andrew); Bishop, J.A.N. (Julia A. N.); K.E. North (Kari); C. Ohlsson (Claes); K.K. Ong (Ken); I. Prokopenko (Inga); Richards, J.B. (J. Brent); E.E. Schadt (Eric); T.D. Spector (Timothy); E. Widen (Elisabeth); C.J. Willer (Cristen); J. Yang (Joanna); Ingelsson, E. (Erik); K.L. Mohlke (Karen); J.N. Hirschhorn (Joel); J.A. Pospisilik (Andrew); M.C. Zillikens (Carola); C.M. Lindgren (Cecilia M.); T.O. Kilpeläinen (Tuomas); R.J.F. Loos (Ruth)

    2016-01-01

    textabstractTo increase our understanding of the genetic basis of adiposity and its links to cardiometabolic disease risk, we conducted a genome-wide association meta-analysis of body fat percentage (BF%) in up to 100,716 individuals. Twelve loci reached genome-wide significance (Po5108), of which e

  7. New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk

    DEFF Research Database (Denmark)

    Lu, Yingchang; Day, Felix R; Gustafsson, Stefan

    2016-01-01

    To increase our understanding of the genetic basis of adiposity and its links to cardiometabolic disease risk, we conducted a genome-wide association meta-analysis of body fat percentage (BF%) in up to 100,716 individuals. Twelve loci reached genome-wide significance (P<5 × 10(-8)), of which eigh...

  8. New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk

    NARCIS (Netherlands)

    Lu, Y.; Groot, de C.P.G.M.; Dhonukshe-Rutten, R.A.M.

    2016-01-01

    To increase our understanding of the genetic basis of adiposity and its links to cardiometabolic disease risk, we conducted a genome-wide association meta-analysis of body fat percentage (BF%) in up to 100,716 individuals. Twelve loci reached genome-wide significance (P<5 × 10−8), of which eight

  9. New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk

    DEFF Research Database (Denmark)

    Lu, Yingchang; Day, Felix R; Gustafsson, Stefan

    2016-01-01

    To increase our understanding of the genetic basis of adiposity and its links to cardiometabolic disease risk, we conducted a genome-wide association meta-analysis of body fat percentage (BF%) in up to 100,716 individuals. Twelve loci reached genome-wide significance (P<5 × 10(-8)), of which eigh...

  10. Microsatellite Analysis of Genetic Diversity Between Loach with Different Levels of Ploidy

    Institute of Scientific and Technical Information of China (English)

    Li Ya-juan; Qi Hong-rui; Ma Hai-yan; Zhou He; Xu Wen; Sui Yi; Li Jia-qi

    2014-01-01

    We used microsatellite markers to investigate the genetic parameters of three different polyploidy populations ofMisgurnus anguillicaudatus from Honghu City, Hubei Province. Polyacrylamide gel electrophoresis banding patterns of diploid (2n), triploid (3n) and tetraploid loaches (4n) were analyzed with PopGen software. A total of 68 alleles were obtained from seven microsatellite loci and the polymorphism information content (PIC) indices were all above 0.5. The average expected mean heterozygosity values (He) were 0.8420, 0.7186 and 0.8521; the average observed mean heterozygosity values (Ho) were 0.9674, 0.9785 and 0.8928; and the Hardy-WeinbergP values were 0.3078, 0.3151 and 0.3762, for diploid, triploid and tetraploid individuals, respectively. The results indicated that the three populations were highly polymorphic, with no deviations from Hardy-Weinberg equilibrium observed at all the seven microsatellite loci. This indicated a high level of genetic diversity within the populations. A cluster analysis diagram showed that the shortest genetic distance was between diploid and tetraploid loaches and they shared a close phylogenetic relationship. The triploid and tetraploid individuals had the most distant phylogenetic relationship.

  11. Microsatellite DNA polymorphism in selectively controlled Apis mellifera carnica and Apis mellifera caucasica populations from Poland

    Directory of Open Access Journals (Sweden)

    Nikolova Stanimila R.

    2015-01-01

    Full Text Available Genetic polymorphism in selectively controlled honeybee populations of A. m. carnica and A. m. caucasica in Poland, was characterized by microsatellite DNA analysis. All honeybee samples were analyzed for nine microsatellite loci: Ac011; A024; A043; A088; Ap226; Ap238; Ap243; Ap249 and Ap256, which were found to be polymorphic in both populations. The mean number of alleles per locus was 6.222 for A. m. carnica and 4.556 for A. m. caucasica. Average observed and expected heterozygosity values were calculated as 0.976 and 0.734 in A. m. carnica and as 0.933 and 0.603 in A. m. caucasica, respectively. For the nine microsatellite loci, a total of 76 alleles were found in both populations. Thirty-five private alleles were observed in A. m. carnica and 20 in A. m. caucasica. Information about allele frequencies, FST values and genotypic differentiation is given. Nei’s genetic distance between studied populations of A. m. carnica and A. m. caucasica was calculated as 0.384.

  12. Isolation and characterization of microsatellite markers for Axonopus compressus (Sw.) Beauv. (Poaceae) using 454 sequencing technology.

    Science.gov (United States)

    Wang, X-L; Li, Y; Liao, L; Bai, C-J; Wang, Z-Y

    2015-05-11

    Axonopus compressus (Sw.) Beauv. is a perennial herb widely used as a garden lawn grass. In this study, we used Roche 454 pyrosequencing, combined with the magnetic bead enrichment method FIASCO, to isolate simple sequence repeat markers from the A. compressus genome. A total of 1942 microsatellite loci were identified, with 53,193 raw sequencing reads. One hundred micro-satellite loci were selected to test the primer amplification efficiency in 24 individuals; 14 primer pairs yielded polymorphic amplification products. The number of observed alleles ranged from two to six, with an average of 3.5. Shannon's Information index values ranged from 0.169 to 0.650, with an average of 0.393. Nei's genetic diversity values ranged from 0.108 to 0.457, with an average of 0.271. This first set of microsatellite markers developed for Axonopus will assist in the development of molecular marker-assisted breeding and the assessment of genetic diversity in A. compressus.

  13. MITOCHONDRIAL AND MICROSATELLITE DNA ANALYSES OF AUSTROPOTAMOBIUS PALLIPES POPULATIONS IN SOUTH TYROL (ITALY AND TYROL (AUSTRIA

    Directory of Open Access Journals (Sweden)

    BARIC S.

    2005-07-01

    Full Text Available Historical data show that the native white-clawed crayfish, Austropotamobius pallipes, was once widespread throughout South Tyrol (northern Italy, whereas recent studies identified only half a dozen remaining populations. In order to implement conservation strategies based on knowledge of genetic diversity, each of the six remaining populations in South Tyrol and one population in Tyrol (Austria were investigated by (i sequencing segments of two mitochondrial DNA genes, 16S rRNA and cytochrome c oxidase subunit I, and (ii by analysing four microsatellite DNA loci. Extremely low degrees of genetic differentiation within and among the South Tyrolean populations of A. pallipes were found with mitochondrial DNA sequences. In contrast, microsatellite data displayed not only substantial genetic structure among populations, but also moderate genetic variability within four out of six populations in South Tyrol. The two remaining populations revealed a complete absence of genetic variability. Moreover, both of these populations as well as the population from Austria were fixed for single alleles at three of the four investigated microsatellite loci. Our data have important conservation implications and also show that mitochondrial DNA is not always a sufficient tool to study crayfish populations on a small geographical scale.

  14. Study of Genetic Diversity in Iranian Turkmen Horse by Four Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    M. Samoozad

    2013-03-01

    Full Text Available The aim of this study was to assess the genetic diversity of Iranian Turkmen Horse using microsatellite markers (HMS02, HMS03, HMS07 and AHT04. Blood samples were collected from 51 Turkmen horses in Khorasan Shomali province, Iran. Genomic DNA was extracted and then standard Polymerase Chain Reaction performed to amplify the microsatellite markers using specific primers. The PCR products were electrophoresed on 8% polyacrylamide gel. The results have demonstrated that the number of alleles in these loci varied from 9 to 12 with mean value of 10.5. HMS02 and HMS07 had the highest (12 and the lowest (9 number of alleles, respectively. HMS02 had the highest (0.8847 and HMS03 had the lowest (0.8039 heterozygosity rates. Also, polymorphic information content (PIC was the highest (0.86 in HMS07and the lowest (0.77 in HMS03. Finally, the highest and the lowest value of Shannon index were estimated in HMS07 and AHT04, respectively. Results have shown that these four microsatellite loci have high polymorphism and can be used as suitable molecular markers in genetic studies.

  15. Microsatellite Development for an Endangered Bream Megalobrama pellegrini (Teleostei, Cyprinidae Using 454 Sequencing

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    Zuogang Peng

    2012-03-01

    Full Text Available Megalobrama pellegrini is an endemic fish species found in the upper Yangtze River basin in China. This species has become endangered due to the construction of the Three Gorges Dam and overfishing. However, the available genetic data for this species is limited. Here, we developed 26 polymorphic microsatellite markers from the M. pellegrini genome using next-generation sequencing techniques. A total of 257,497 raw reads were obtained from a quarter-plate run on 454 GS-FLX titanium platforms and 49,811 unique sequences were generated with an average length of 404 bp; 24,522 (49.2% sequences contained microsatellite repeats. Of the 53 loci screened, 33 were amplified successfully and 26 were polymorphic. The genetic diversity in M. pellegrini was moderate, with an average of 3.08 alleles per locus, and the mean observed and expected heterozygosity were 0.47 and 0.51, respectively. In addition, we tested cross-species amplification for all 33 loci in four additional breams: M. amblycephala, M. skolkovii, M. terminalis, and Sinibrama wui. The cross-species amplification showed a significant high level of transferability (79%–97%, which might be due to their dramatically close genetic relationships. The polymorphic microsatellites developed in the current study will not only contribute to further conservation genetic studies and parentage analyses of this endangered species, but also facilitate future work on the other closely related species.

  16. Combining ability of twelve maize populations

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    Vacaro Elton

    2002-01-01

    Full Text Available Genetic progress depends on germplasm quality and breeding methods. Twelve maize populations and their crosses were evaluated to estimate combining ability and potential to be included as source populations in breeding programs. Plant height, point of insertion of the first ear, number of ears per plant, number of grains per ear, root and stalk lodging and grain yield were studied in two locations in Brazil, during the 1997/98 season. Genotype sum of squares was divided into general (GCA and specific (SCA combining ability. Results indicated the existence of genetic divergence for all traits analyzed, where additive effects were predominant. The high heterosis levels observed, mainly in Xanxerê, suggested the environmental influence on the manifestation of this genetic phenomenon. Populations revealed potential to be used in breeding programs; however, those more intensively submitted to selection could provide larger genetic progress, showing the importance of population improvement for the increment of the heterosis in maize.

  17. Rapid, economical single-nucleotide polymorphism and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod Gadus morhua.

    Science.gov (United States)

    Carlsson, J; Gauthier, D T; Carlsson, J E L; Coughlan, J P; Dillane, E; Fitzgerald, R D; Keating, U; McGinnity, P; Mirimin, L; Cross, T F

    2013-03-01

    By combining next-generation sequencing technology (454) and reduced representation library (RRL) construction, the rapid and economical isolation of over 25 000 potential single-nucleotide polymorphisms (SNP) and >6000 putative microsatellite loci from c. 2% of the genome of the non-model teleost, Atlantic cod Gadus morhua from the Celtic Sea, south of Ireland, was demonstrated. A small-scale validation of markers indicated that 80% (11 of 14) of SNP loci and 40% (6 of 15) of the microsatellite loci could be amplified and showed variability. The results clearly show that small-scale next-generation sequencing of RRL genomes is an economical and rapid approach for simultaneous SNP and microsatellite discovery that is applicable to any species. The low cost and relatively small investment in time allows for positive exploitation of ascertainment bias to design markers applicable to specific populations and study questions.

  18. 利用微卫星标记分析湖羊GDF8区域的遗传多样性%Genetic Polymorphism in GDF8 Region of HU Sheep Based on Microsatellite DNA

    Institute of Scientific and Technical Information of China (English)

    吴文忠; 钱建共; 陈玲; 孙伟

    2009-01-01

    [Objective] This study was to analyze the genetic polymorphism in GDF8 Region of HU sheep. [Method] Four microsatellite loci including BMS1591, TEXAN-2, FCB128 and BM81124 mapped on GDF8 region of chromosome No. 2 of sheep that may be correlated with growth performance were chosen to detect the molecular genetics foundation of growth performance of Hu sheep. [Result] Four microsatellite loci detected were high in heterozygosity, more in effective alleles number and rich in polymorphic information, all the three indices passed through the high polymorphic level (PIC>0.5). [Conclusion] The four microsatellite loci detected could be used to estimate the genetic polymorphism of growth performance of Hu sheep.

  19. 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

  20. Characterization of microsatellites for population genetic analyses of the fungus-growing termite Odontotermes formosanus (Isoptera: Termitidae).

    Science.gov (United States)

    Husseneder, Claudia; Garner, Susan P; Huang, Qiuying; Booth, Warren; Vargo, Edward L

    2013-10-01

    The fungus-growing subterranean termite Odontotermes formosanus Shiraki (Isoptera: Termitidae) is a destructive pest in Southeast Asia. To facilitate studies on the biology, ecology, and control of O. formosanus, we isolated and characterized nine novel microsatellite loci from a mixed partial genomic library of O. formosanus and the sympatric Macrotermes barneyi Light enriched for di-, tri-, and tetranucleotide repeats. We screened these loci in three populations of O. formosanus from China. All loci were polymorphic. Three loci showed heterozygote deficit possibly because of the presence of null alleles. The remaining six loci with 4-15 alleles per locus and an average observed heterozygosity of 0.15-0.60 across populations were used for population genetic analysis. Populations from different provinces (Guangdong, Jiangxi, and Hubei) were genetically differentiated, but the genetic distance between populations was surprisingly small (FST: 0.03-0.08) and the gene flow was considerable (Nem: 3-8), despite the geographical distance being >300 km. Genetic diversity within populations was low (allelic richness: 5.1-6.3) compared with other subterranean dwelling termites, but consistent with the diversity in species of the family Termitidae. Microsatellite markers developed for O. formosanus will allow further studies to examine the phylogeography, population genetic and colony breeding structure, dispersal ranges, and size of foraging territories in this and closely related species, as well as aid in assessing treatment success.