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.

scholarly journals VARIANCE COMPONENT ANALYSIS OF ALLOZYME FREQUENCY DATA FROM EASTERN POPULATIONS OF DROSOPHILA MELANOGASTER

Genetics ◽  
1978 ◽  
Vol 88 (1) ◽  
pp. 121-137
Author(s):  
Diana B Smith ◽  
Charles H Langley ◽  
Frank M Johnson
Keyword(s):  
North Carolina ◽  
Variance Component ◽  
Low Frequency ◽  
The United States ◽  
Null Alleles ◽  
Variance Component Analysis ◽  
Frequency Variation ◽  
Nonrandom Mating ◽  
Component Estimation ◽  
Allozyme Loci

ABSTRACT Gene frequency variation at eight polymorphic allozyme loci in Drosophila meianogaster populations in North Carolina and the east coast of the United States were analyzed utilizing the variance component estimation procedures suggested by COCKERHAM (1969, 1973). These variance components were used to estimate correlations of genes within small geographic regions. The average (over loci) correlation between genes in the same individual within subpopulations was estimated to be 0.033. That between genes in the same subpopulation in different individuals was estimated to be very small, although significantly different from zero. The macrogeographic variation measured by the correlation of genes sampled from the same local region was large for some loci and smaller for others. This variation was also analyzed by correlation with latitude and longitude. Several previously recognized clines were identified as were several new clines.—These results were interpreted as indicating either some degree of nonrandom mating and locel breeding unit isolation or a low frequency of null alleles. The geographic and temporal variation has no simple interpretation.

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 Validation and characterization of thirteen microsatellite markers for queen conch, Lobatus gigas

2016 ◽  
Author(s):  
Nathan K Truelove ◽  
Loong Fai Ho ◽  
Richard F Preziosi ◽  
Stephen J. Box
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Null Allele ◽  
Florida Keys ◽  
Illumina Miseq ◽  
Allele Frequencies ◽  
Null Alleles ◽  
Queen Conch ◽  
Hardy Weinberg Equilibrium

We report the development and characterization of 13 novel microsatellite loci for the Caribbean queen conch, Lobatus gigas, an ecologically and commercially important marine gastropod. Paired-end sequencing was carried out on genomic DNA from a single queen conch using half a flow cell lane of an Illumina MiSeq. A total of 48 potentially amplifiable loci containing microsatellites were tested on 45 individuals from the Florida Keys and Bahamas. In total, 13 consistently amplifying and polymorphic microsatellite loci were identified. The number of alleles ranged from 4 to 26 and observed heterozygosities ranged from 0.340 to 1.00. There was no evidence of scoring error, large allele dropout, or evidence of linkage disequilibrium at any locus. Four loci deviated from Hardy-Weinberg equilibrium due to moderate levels of null alleles (null allele frequencies ranged from 0.081 to 0.230). Although null alleles were detected at four microsatellite loci, the high levels of polymorphism and moderate null allele frequencies suggest that these 13 novel microsatellite markers will be useful for researchers carrying out conservation genetic studies of L. gigas.

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.

Characterization of a New Set of Microsatellite Markers Suggests Polygyny and Polyandry in Atta cephalotes (Hymenoptera: Formicidae)

2020 ◽  
Vol 113 (6) ◽  
pp. 3021-3027
Author(s):  
Vanessa Muñoz-Valencia ◽  
Kirsi Kähkönen ◽  
James Montoya-Lerma ◽  
Fernando Díaz
Keyword(s):  
Social Structure ◽  
Microsatellite Markers ◽  
Preliminary Analysis ◽  
Null Alleles ◽  
Atta Cephalotes ◽  
Genetic Studies ◽  
Leaf Cutting ◽  
Polymorphic Microsatellite ◽  
Population Viscosity

Abstract The leaf-cutting ant, Atta cephalotes L. (1758), is a major herbivore with great economic impact in the Neotropics. Because of its broad range and human-mediated dissemination, the ecology of this ant has received considerable attention; however, questions concerning its population genetics, dispersal, and social structure remain unexplored. Here, we aimed to identify and provide information on molecular and statistical performance of a suite of polymorphic microsatellite markers for A. cephalotes while demonstrating their utility for further genetic studies. We designed primer sequences targeting thousands of microsatellite loci and then screened 30 of these for amplification and polymorphism. Fifteen of these loci were selected and used to evaluate their polymorphism using 74 ants sampled from 15 different nests of the same location. This set of 15 loci exhibited variation of 2–20 alleles, with a mean heterozygosity of 0.57. All loci followed Hardy–Weinberg expectations with no evidence of linkage disequilibrium, while two loci showed evidence of null alleles. Our preliminary analysis suggested substantial nest differentiation with no population viscosity within the sampled location, as well as colonies with multiple queens (polygyny) and paternity (polyandry). Our newly identified microsatellites have proven to be highly informative to investigate gene flow, social structure and reproduction of this key agricultural pest.

scholarly journals Isolation and Characterization of Twenty Polymorphic Microsatellite Loci for Moringa oleifera (Moringaceae)

HortScience ◽  
2010 ◽  
Vol 45 (4) ◽  
pp. 690-692 ◽  
Author(s):  
Jiang-Chong Wu ◽  
Jing Yang ◽  
Zhi-Jian Gu ◽  
Yan-Ping Zhang
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Population Genetic ◽  
Moringa Oleifera ◽  
Microsatellite Primers ◽  
Genetic Studies ◽  
Isolation And Characterization ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite

By using a modified biotin-streptavidin capturing method, a total of 20 polymorphic microsatellite markers were developed from Moringa oleifera Lam. (Moringaceae), a useful multipurpose tree. Twenty-four domesticated individuals, with germplasms of India and Myanmar, were used to screen polymorphism of these 20 microsatellite markers. The number of alleles per locus ranged from two to six. The expected and observed heterozygosity varied from 0.3608 to 0.7606 and from 0.0000 to 0.8750, respectively. Seven loci were significantly deviated from Hardy-Weinberg equilibrium. The availability of these microsatellite primers would provide a powerful tool for aspects of detailed population genetic studies of M. oleifera.

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.

scholarly journals Development and characterisation of polymorphic microsatellite markers in the pearl oyster Pteria penguin (Roding, 1798)

2016 ◽  
Vol 63 (4) ◽  
Author(s):  
Nan Zhang ◽  
Zhenhua Ma ◽  
Dianchang Zhang ◽  
Huayang Guo ◽  
Lin Lin ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Microsatellite Markers ◽  
Pearl Oyster ◽  
Significant Linkage Disequilibrium ◽  
Genetic Studies ◽  
Pteria Penguin ◽  
Conservation Genetic ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
Significant Linkage

We developed and characterised 12 polymorphic microsatellite loci for Pteria penguin (Roding, 1798), an important pearl oyster species for pearl production in China. The number of observed alleles per locus ranged from 5 to 26 within 46 individuals. The observed and expected heterozygosities per locus ranged from 0.2 to 0.925 and 0.707 to 0.945, respectively. The polymorphism information content values per locus ranged from 0.656 to 0.929. Ten loci were in accordance with Hardy-Weinberg equilibrium and no significant linkage disequilibrium was detected between loci. These new microsatellite markers will be useful for population and conservation genetic studies of P. penguin.

scholarly journals Validation and characterization of thirteen microsatellite markers for queen conch, Lobatus gigas

2016 ◽  
Author(s):  
Nathan K Truelove ◽  
Loong Fai Ho ◽  
Richard F Preziosi ◽  
Stephen J. Box
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Null Allele ◽  
Florida Keys ◽  
Illumina Miseq ◽  
Allele Frequencies ◽  
Null Alleles ◽  
Queen Conch ◽  
Hardy Weinberg Equilibrium

We report the development and characterization of 13 novel microsatellite loci for the Caribbean queen conch, Lobatus gigas, an ecologically and commercially important marine gastropod. Paired-end sequencing was carried out on genomic DNA from a single queen conch using half a flow cell lane of an Illumina MiSeq. A total of 48 potentially amplifiable loci containing microsatellites were tested on 45 individuals from the Florida Keys and Bahamas. In total, 13 consistently amplifying and polymorphic microsatellite loci were identified. The number of alleles ranged from 4 to 26 and observed heterozygosities ranged from 0.340 to 1.00. There was no evidence of scoring error, large allele dropout, or evidence of linkage disequilibrium at any locus. Four loci deviated from Hardy-Weinberg equilibrium due to moderate levels of null alleles (null allele frequencies ranged from 0.081 to 0.230). Although null alleles were detected at four microsatellite loci, the high levels of polymorphism and moderate null allele frequencies suggest that these 13 novel microsatellite markers will be useful for researchers carrying out conservation genetic studies of L. gigas.

Improving genetic monitoring of the northern hairy-nosed wombat (Lasiorhinus krefftii)

2014 ◽  
Vol 62 (3) ◽  
pp. 246 ◽  
Author(s):  
Lauren C. White ◽  
Alan Horsup ◽  
Andrea C. Taylor ◽  
Jeremy J. Austin
Keyword(s):  
Microsatellite Markers ◽  
Dna Analysis ◽  
Genotype Frequencies ◽  
Abundance Estimates ◽  
Multiplex Reaction ◽  
Hardy Weinberg Equilibrium ◽  
Genetic Techniques ◽  
Polymerase Chain ◽  
Future Population

The endangered northern hairy-nosed wombat (Lasiorhinus krefftii) has been monitored via remote sampling and genetic techniques since 2000, thus avoiding the detrimental effects on the animals of trapping and increasing the precision of abundance estimates. The currently available dinucleotide microsatellite markers used for this task are prone to stutter and other polymerase chain reaction artefacts, making allele calling difficult, and requiring costly duplication to ensure accuracy. To remedy this we have developed eight new tri- and tetranucleotide microsatellite markers that reduce the problem of stutter in DNA analysis. These new markers, along with three of the existing markers (two microsatellites and the SRY gender marker) were optimised in a single multiplex reaction that will reduce the time and cost of future northern hairy-nosed wombat hair censuses. We tested this new multiplex on 277 non-invasively collected hairs. One locus was rejected due to null-allele issues. The remaining nine microsatellite loci had two or three alleles. Genotype frequencies in the sample of detected individuals did not differ significantly from Hardy–Weinberg equilibrium and there was no evidence of linkage disequilibrium. This new multiplex provides comparable power to distinguish individuals, fewer issues with stutter artefacts and a reduced time and cost of analysis. It will be useful for future population censuses and long-term monitoring of individuals once they have been scored in previously genotyped and assigned samples.

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