scholarly journals A core set of microsatellite markers identified for use in population genetic studies of Purple Swamphen (Porphyrio porphyrio)

2012 ◽  
Vol 35 (1) ◽  
pp. 23-26
Author(s):  
S. A. Subrata ◽  
◽  
I. Storch ◽  
Keyword(s):  
Microsatellite Markers ◽  
Population Genetic ◽  
Polymorphic Information Content ◽  
Null Alleles ◽  
Genetic Studies ◽  
Gametic Disequilibrium ◽  
Core Set ◽  
Porphyrio Porphyrio ◽  
Candidate Loci ◽  
Significant Linkage

Populations of Purple Swamphen have been declining in some parts of the world due to wetland degradation and poaching. Conservation efforts might benefit from population genetic studies using microsatellite markers. Here we describe the selection of microsatellite markers suitable for such studies. We tested the markers against the evidence of the null alleles and gametic disequilibrium. From fourteen candidate loci, ten displayed a null alleles frequency of less than 0.2 and had no significant linkage disequilibrium. The selected loci showed no deviation from HWE and had a mean polymorphic information content of 0.516. Based on the test, we suggest these loci are suitable for population genetic studies of the species.

Development of microsatellite markers for the short-beaked echidna using three different approaches

2009 ◽  
Vol 57 (4) ◽  
pp. 219 ◽  
Author(s):  
C. Vanpé ◽  
E. Buschiazzo ◽  
J. Abdelkrim ◽  
G. Morrow ◽  
S. C. Nicol ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Population Genetic ◽  
High Probability ◽  
Genomic Library ◽  
Polymorphic Information Content ◽  
Null Alleles ◽  
Genomic Sequencing ◽  
Expected Heterozygosity ◽  
Study Population ◽  
Using Data

We used three different methods, size-selected genomic library, cross-species amplification of a mammal-wide set of conserved microsatellites and genomic sequencing, to develop a panel of 43 microsatellite loci for the short-beaked echidna (Tachyglossus aculeatus). These loci were screened against 13 individuals from three different regions (Tasmania, Kangaroo Island, Perth region), spanning the breadth of the range of the short-beaked echidna. Nine of the 43 tested loci amplified reliably, generated clear peaks on the electropherogram and were polymorphic, with the number of alleles per locus ranging from two to eight (mean = 3.78) in the individuals tested. Polymorphic information content ranged from 0.16 to 0.78, and expected heterozygosity ranged from 0.19 to 0.84. One of the nine microsatellites showed a heterozygote deficit, suggesting a high probability of null alleles. The genomic sequencing approach using data derived from the Roche FLX platform is likely to provide the most promising method to develop echidna microsatellites. The microsatellite markers developed here will be useful tools to study population genetic structure, gene flow, kinship and parentage in Tachyglossus sp. and potentially also in endangered Zaglossus species.

scholarly journals Genetic diversity and differentiation in reef-buildingMilleporaspecies, as revealed by cross-species amplification of fifteen novel microsatellite loci

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2936 ◽  
Author(s):  
Caroline E. Dubé ◽  
Serge Planes ◽  
Yuxiang Zhou ◽  
Véronique Berteaux-Lecellier ◽  
Emilie Boissin
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Natural Populations ◽  
454 Sequencing ◽  
Genetic Distances ◽  
Null Alleles ◽  
Future Research ◽  
Significant Linkage ◽  
Pacific Species

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 coralMillepora platyphylla, an important reef-builder of Indo-Pacific reefs.We tested the cross-species amplification of these loci in five other species of the genusMilleporaand 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 speciesM. platyphylla,among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five otherMilleporaspecies 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 speciesM. complanatadue 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 ofMillepora.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 hydrozoanMilleporaspecies creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

scholarly journals Microsatellite markers for population genetic studies of the blowfly Chrysomya putoria (Diptera: Calliphoridae)

2009 ◽  
Vol 104 (7) ◽  
pp. 1047-1050 ◽  
Author(s):  
Rosangela Aparecida Rodrigues ◽  
Ana Maria Lima de Azeredo-Espin ◽  
Tatiana Teixeira Torres
Keyword(s):  
Microsatellite Markers ◽  
Population Genetic ◽  
Genetic Studies

Microsatellite markers of Gonystylus bancanus (Thymelaeaceae) for population genetic studies and DNA fingerprinting

2009 ◽  
Vol 1 (1) ◽  
pp. 153-157 ◽  
Author(s):  
Kevin Kit Siong Ng ◽  
Soon Leong Lee ◽  
Chin Hong Ng ◽  
Lee Hong Tnah ◽  
Chai Ting Lee ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Dna Fingerprinting ◽  
Population Genetic ◽  
Genetic Studies

Cross-species amplification and characterization of microsatellite loci in Pinus mugo Turra

Biologia ◽  
2013 ◽  
Vol 68 (4) ◽  
Author(s):  
Konrad Celiński ◽  
Ewa Pawlaczyk ◽  
Aleksandra Wojnicka-Półtorak ◽  
Ewa Chudzińska ◽  
Wiesław Prus-Głowacki
Keyword(s):  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Pinus Mugo ◽  
Genetic Studies ◽  
Transfer Rates ◽  
Isolation And Characterization ◽  
Nuclear Microsatellite ◽  
European Mountain ◽  
High Level

AbstractPinus mugo (dwarf mountain pine) is an important component of European mountain ecosystems. However, little is known about the present genetic structure and population differentiation of this species at the DNA level, possibly due to a lack of nuclear microsatellite markers (SSR) developed for Pinus mugo. Therefore in this study we transferred microsatellite markers originally developed for Pinus sylvestris and Pinus taeda to Pinus mugo. This cross-species amplification approach is much faster and less expensive than isolation and characterization of new microsatellite markers. The transfer rates from the source species to Pinus mugo were moderately low (26%). There were no differences in microsatellite repeat motifs between the source species and Pinus mugo. Nuclear microsatellite markers successfully transferred to Pinus mugo can be applied to various genetic studies on this species, due to the high level of their polymorphism and high value of polymorphic information content.

scholarly journals Development of microsatellite markers for the house cricket, Acheta domesticus (Orthoptera: Gryllidae)

2020 ◽  
Vol 21 (9) ◽  
Author(s):  
Yash Munnalal Gupta ◽  
SUPATCHAREE TANASARNPAIBOON ◽  
KITTISAK BUDDHACHAT ◽  
SURIN PEYACHOKNAGUL ◽  
PHATTHARAPORN INTHIM ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Analysis ◽  
Microsatellite Markers ◽  
Population Genetic ◽  
Acheta Domesticus ◽  
House Cricket ◽  
Population Genetic Analysis ◽  
Closely Related Species ◽  
Genetic Studies ◽  
Future Population

Abstract. Gupta YM, Tanasarnpaiboon S, Buddhachat K, Peyachoknagul S, Inthim P, Homchan S. 2020. Development of microsatellite markers for the house cricket, Acheta domesticus (Orthoptera: Gryllidae). Biodiversitas 21: 4094-4099. The house cricket, Acheta domesticus, is one of the species of crickets commonly found in Thailand. Insect breeders in Thailand prefer to breed house cricket as food due to its better taste and popularity among local people. Moreover, largescale breeding industries also breed house cricket to produce cricket-based edible products. Insect breeding industry is growing rapidly and requires primary precaution for sustainable production. To facilitate breeding system to maintain genetic variation in the captive population, we have sequenced the whole genome of A. domesticus to search for simple sequence repeats (SSRs) in order to develop polymorphic microsatellite markers for preliminary population genetic analysis. A total of 112,157 SSRs with primer pairs were identified in our analysis.  Of these, 91 were randomly selected to check for amplification of microsatellite polymorphisms. From these, nine microsatellites were used to check genetic variation in forty-five individuals of A. domesticus from the Phitsanulok population (Thailand).  These microsatellite markers also showed cross-amplification with other three species of edible crickets, specifically Gryllus bimaculatus, Gryllus testaceus, and Brachytrupes portentosus. The microsatellite markers presented herein will facilitate future population genetic analysis of A. domesticus populations. Moreover, the transferability of these makers would also enable researchers to conduct genetic studies for other closely related species.

scholarly journals Development of microsatellite markers for the critically endangered conifer Glyptostrobus pensilis (Cupressaceae) using transcriptome data

2019 ◽  
Vol 68 (1) ◽  
pp. 41-44 ◽  
Author(s):  
Xin-Yu Li ◽  
Xue-Ying Lin ◽  
Markus Ruhsam ◽  
Lu Chen ◽  
Xing-Tong Wu ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Related Species ◽  
Population Genetic ◽  
Critically Endangered ◽  
Transcriptome Data ◽  
Genetic Studies ◽  
Chinese Populations ◽  
Expected Heterozygosity ◽  
Ssr Loci ◽  
Hardy Weinberg Equilibrium

Abstract Glyptostrobus pensilis (Cupressaceae) is a critically endangered conifer which occurs in China, Laos, and Vietnam where it is only known from a few populations. Here we aim to develop microsatellite markers which can be used to study the genetic variation within this species. Using transcriptome data we tested 170 SSR loci for polymorphism in 16 samples. Twenty-three loci were polymorphic and selected for the genetic analysis of 83 individuals from three Chinese populations. The number of alleles per locus and population ranged from one to eight, the observed and expected heterozygosity from Ho = 0.00-1.00 and He = 0.00-0.83, respectively. Fifteen loci deviated from Hardy-Weinberg equilibrium in at least one of the three populations. The majority of loci could also be successfully amplified in four related species, namely Cryptomeria fortunei, Taxodium distichum, Taxodium ascendens and Cunninghamia lanceolata. These developed microsatellites are suitable for population genetic studies of Glyptostrobus pensilis and related species.

scholarly journals Transferability of Microsatellite Markers Developed in Oenothera spp. to the Invasive Species Oenothera drummondii Hook. (Onagraceae)

Diversity ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 387
Author(s):  
Raquel Hernández-Espinosa ◽  
Jorge González-Astorga ◽  
Alejandro Espinosa de los Monteros ◽  
Dánae Cabrera-Toledo ◽  
Juan B. Gallego-Fernández
Keyword(s):  
Invasive Species ◽  
North Carolina ◽  
Microsatellite Markers ◽  
Coastal Dunes ◽  
The United States ◽  
Null Alleles ◽  
Genetic Studies ◽  
Native Populations ◽  
Hardy Weinberg Equilibrium ◽  
Future Population

Oenothera drummondii Hook. (Onagraceae) has life-history traits that make it an invasive species. Native populations are distributed along the coastal dunes from North Carolina in the United States to Tabasco in the Gulf of Mexico. It has been reported as an invasive species in Spain, Israel, and China, where this species can successfully colonize and dominate if the environmental conditions are appropriate. In South Africa, Australia, New Zealand, and France, it is reported to be naturalized. In this study, 28 microsatellite markers developed for other Oenothera species were evaluated for cross-amplification in O. drummondii. Nine primers showed consistent amplification and were polymorphic. Polymorphism was assessed in three populations from both native and invaded areas. Results indicated generalized low genetic variability. Three loci showed significant deviations from the Hardy Weinberg equilibrium, associated with null alleles’ presence. The observed heterozygosity and inbreeding coefficient reflected a generalized excess of homozygotes, particularly in the invaded population “El Dique”, likely due to allele fixation. High genetic differentiation was found between the three populations. These results highlight the accuracy of these markers for future population genetic studies in O. drummondii.

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