New Microsatellite Markers for Two Sympatric Tinamou Species, the Ornate Tinamou (Nothoprocta ornata) and Darwin's Nothura (Nothura darwinii)

Tinamous (Tinamidae) represent one of the most ancient living avian lineages but their life history traits are relatively unstudied. Here we identified microsatellite loci for two sympatric tinamou species, the Ornate Tinamou ( Nothoprocta ornata) and the Darwin's Nothura ( Nothura darwinii) from low coverage Illumina sequencing of genomic DNA. The experiment yielded a large number of candidate loci. We designed primers and tested them for successful amplification in 1 to 2 populations of the target species, tested for deviation from the Hardy–Weinberg equilibrium and the presence of null alleles, the levels of polymorphism and potential cross-amplification. All 30 and 24 loci amplified consistently, in the Ornate Tinamou and in Darwin's Nothura, respectively. In the Ornate Tinamou, 25 loci were polymorphic and in the Darwin's Nothura 12, with 2 to 14 alleles per locus in both species. The expected heterozygosity ranged from 0.054 to 0.917 in the Ornate Tinamou and from 0.044 to 0.908 in the Darwin's Nothura. 23 (40%) of 54 loci were successfully cross-amplified. These newly discovered, polymorphic microsatellite loci represent a valuable tool for future studies on social behaviour, parentage and genetic population structure in tinamous.

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Population genetics of the fish Brycon henni (Characiformes: Bryconidae) using species-specific polymorphic microsatellite loci

Revista de Biología Tropical ◽

10.15517/rbt.v68i3.38405 ◽

2020 ◽

Vol 68 (3) ◽

Author(s):

Ricardo M. Landínez-García ◽

Edna J. Márquez

Keyword(s):

Population Genetics ◽

Microsatellite Loci ◽

Genomic Library ◽

International Union ◽

Genetic Population ◽

Genetic Diversity And Structure ◽

Polymorphic Microsatellite ◽

Species Specific ◽

Low Coverage ◽

Risk Categorization

Introduction: The freshwater fish Brycon henni (Characiformes: Bryconidae) is endemic to Colombia and currently considered as “least concern” according to the International Union for Conservation of Nature (IUCN). Objective: To develop microsatellite markers to examine population genetics in Brycon henni. Methods: Using a low-coverage sequenced genomic library, this study developed the first set of microsatellite loci to study the population genetics of this Neotropical species. These loci were used to evaluate the genetic diversity and structure of B. henni from three sites of the Magdalena-Cauca Basin (Colombia). Results: A set of twenty-one polymorphic microsatellite loci was highly informative and revealed that B. henni is evenly genetically structured between two tributaries of the Cauca River separated by only 30 km, a finding that indicates it conforms to reproductively isolated groups. Conclusions: We reported a set of twenty-one polymorphic microsatellite loci that was highly informative and allowed the detection of genetic structure at local and regional scales. This genetic population structure, concordant with that found in eight congeners, is relevant to estimate the B. henni risk categorization as well as for management, conservation, and restocking programs.

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Development and characterization of new polymorphic microsatellite loci for Trionyx triunguis (Testudines: Trionychidae) in the Mediterranean Basin

Amphibia-Reptilia ◽

10.1163/15685381-00003003 ◽

2015 ◽

Vol 36 (3) ◽

pp. 318-324 ◽

Cited By ~ 1

Author(s):

Özgür Güçlü ◽

Salih Hakan Durmuş ◽

Kamil Candan ◽

Nurettin Beşer ◽

Süheyla Türkyilmaz ◽

...

Keyword(s):

Microsatellite Loci ◽

Captive Breeding ◽

Null Alleles ◽

Enriched Library ◽

Hardy Weinberg Equilibrium ◽

Polymorphic Microsatellite ◽

The Mediterranean ◽

Captive Breeding Programs

The Mediterranean subpopulation of T. triunguis has been listed by IUCN as critically endangered (European Reptile and Amphibian Specialist Group 1996, category CR C2A). There are very few studies for determination of distribution and population genetics of this species in the world. A total of 13 polymorphic microsatellite loci were isolated from 42 samples of T. triunguis by using biotinylated (GT)10, (CT)10, (GATA)5-enriched library. The range of observed heterozygosities was 0.000-0.833 with a mean of 0.274, and the range of expected heterozygosities was 0.081-0.607 with a mean of 0.374. It was found that four loci deviated significantly from Hardy-Weinberg equilibrium after Bonferroni correction analysis. There was no evidence for large allele dropout. Null alleles may be present at ttmed-6, ttmed-8, and ttmed-9 loci, as suggested by the general excess of homozygote for most allele size classes. Designed microsatellite loci could provide a powerful tool for the population structure and conservation genetics studies of the Nile soft-shelled turtle and for captive breeding programs or to detect species illegal trade.

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Isolation and Characterization of Polymorphic Microsatellite Markers for Two Subterranean Termites

Sociobiology ◽

10.13102/sociobiology.v64i3.1692 ◽

2017 ◽

Vol 64 (3) ◽

pp. 352 ◽

Cited By ~ 1

Author(s):

Yu-Lei Dang ◽

Hong-Gui Zhang ◽

Yu-Feng Meng ◽

Min Zhang ◽

Sha Zhao ◽

...

Keyword(s):

Microsatellite Markers ◽

Microsatellite Loci ◽

Population Genetic ◽

Subterranean Termites ◽

Polymorphic Markers ◽

Isolation And Characterization ◽

Expected Heterozygosity ◽

Hardy Weinberg Equilibrium ◽

Polymorphic Microsatellite

We isolated 15 and 18 highly polymorphic genomic microsatellite markers from two subterranean termites, Reticulitermes aculabialis and R. labralis, respectively. A total of 53 alleles were detected in 15 microsatellite loci of R. aculabialis, and the alleles were 3.533±1.302 (mean±SD), while the corresponding data of R. labralis were 115 detected alleles in 18 microsatellite loci with 6.389±1.754 alleles. The observed and expected heterozygosity was 0.496±0.236 and 0.564±0.125 in R. aculabialis, and 0.368±0.263 and 0.702±0.115 in R. labralis, respectively. Seven loci were highly polymorphic (PIC>0.5) in R. aculabialis, and 15 loci were highly polymorphic (PIC>0.5) in R. labralis. All loci showed Hardy–Weinberg equilibrium. These polymorphic markers provide useful tools for population genetic and breeding system studies of subterranean termites.

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Characterization of new polymorphic microsatellite loci for the lesser tree frog (Dendropsophus minutus)

Amphibia-Reptilia ◽

10.1163/15685381-00002974 ◽

2015 ◽

Vol 36 (1) ◽

pp. 83-86

Author(s):

Hilton M. Oyamaguchi ◽

Ryo P. Okubo ◽

Hilton M. Oyamaguchi ◽

Ryo P. Okubo ◽

...

Keyword(s):

Microsatellite Loci ◽

Taxonomic Status ◽

Tree Frog ◽

Expected Heterozygosity ◽

Scale Population ◽

Hardy Weinberg Equilibrium ◽

Taxonomic Confusion ◽

Polymorphic Microsatellite ◽

Roche 454

Dendropsophus minutus is a widely distributed species in South America and presents great phenotypic variation which has led to taxonomic confusion. Herein we describe nine microsatellite loci for D. minutus discovered by genomic shotgun sequencing using Roche 454 pyrosequencing. These microsatellite loci were tested on a panel of 29 individuals. All nine loci were polymorphic (11-22 alleles) with observed heterozygosity ranging from 0.42 to 0.90 and expected heterozygosity from 0.75 to 0.94. Three loci deviated from the Hardy-Weinberg equilibrium. These characterized polymorphic markers for D. minutus will enable investigation of fine scale population structure, evolutionary processes, and clarify taxonomic status. This genetic information will be useful in conservation decisions regarding on this apparently wide distributed species.

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Development of 11 Polymorphic Microsatellite Loci from Primula amthystina Franchet. (Primulaceae)

HortScience ◽

10.21273/hortsci.45.1.148 ◽

2010 ◽

Vol 45 (1) ◽

pp. 148-149

Author(s):

Yuan Huang ◽

Xue-qin Wang ◽

Chun-yan Yang ◽

Chun-lin Long

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Loci ◽

Southwest China ◽

Herbaceous Plant ◽

Genetic Population ◽

Weinberg Equilibrium ◽

Perennial Herbaceous Plant ◽

Hardy Weinberg Equilibrium ◽

Polymorphic Microsatellite

Primula amethystina Franchet. is a beautiful perennial herbaceous plant locally endemic to the alpine area in southwest China. We isolated and characterized 11 polymorphic microsatellite primer pairs from this species. The number of alleles ranged from two to five. The observed and expected heterozygosities (HO and HE) were 0.25 to 0.875 and 0.223 to 0.691, respectively. Six loci were significantly deviated from Hardy-Weinberg equilibrium as a result of the heterozygote deficiency. These markers will have great potential to reveal the genetic population structure and genetic diversity of P. amethystina.

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Polymorphic Microsatellite Loci in the Independent-founding Wasp Polists versicolor (Hymenoptera: Vespidae)

Sociobiology ◽

10.13102/sociobiology.v63i2.899 ◽

2016 ◽

Vol 63 (2) ◽

pp. 845

Author(s):

Yumi Takahashi ◽

Ayano Yamada ◽

Sidnei Mateus ◽

Ronaldo Zucchi ◽

Fabio Nascimento ◽

...

Keyword(s):

Social Interactions ◽

Microsatellite Loci ◽

Genetic Relatedness ◽

Conflicts Of Interest ◽

Microsatellite Primers ◽

Expected Heterozygosity ◽

Polistes Wasps ◽

Polymorphic Microsatellite ◽

Genetic Conflicts ◽

Data Banks

Microsatellite primers developed for a given species are sometimes useful for another in the same genus, making possible to search for pre-existing suitable primers in the data banks such as GenBank. We examined whether existing primers developed for Polistes wasps could be used for the independent-founding wasp Polistes versicolor. We tested 50 microsatellite primers from three Polistes species and found that five microsatellite loci show polymorphism in size in P. versicolor. These five loci were highly polymorphic, having four to 10 alleles in P. versicolor with an expected heterozygosity of 0.530–0.836. These loci can be used to study parameters concerning genetic relatedness such as social interactions in colonies and genetic conflicts of interest among nestmate individuals.

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Development and characterization of twelve new polymorphic microsatellite loci in the Iberian ribbed newt, Pleurodeles waltl (Caudata: Salamandridae), with data on cross-amplification in P. nebulosus

Amphibia-Reptilia ◽

10.1163/15685381-00002926 ◽

2014 ◽

Vol 35 (1) ◽

pp. 129-134 ◽

Cited By ~ 4

Author(s):

Jorge Gutiérrez-Rodríguez ◽

Elena G. Gonzalez ◽

Íñigo Martínez-Solano

Keyword(s):

Population Dynamics ◽

Microsatellite Loci ◽

Evolutionary History ◽

The Novel ◽

Expected Heterozygosity ◽

History Of ◽

Southern Iberia ◽

Polymorphic Microsatellite ◽

Pleurodeles Waltl

Twelve novel polymorphic microsatellite loci were isolated and characterized for the Iberian ribbed newt, Pleurodeles waltl (Caudata, Salamandridae). The distribution of this newt ranges from central and southern Iberia to northwestern Morocco. Polymorphism of these novel loci was tested in 40 individuals from two Iberian populations and compared with previously published markers. The number of alleles per locus ranged from two to eight. Observed and expected heterozygosity ranged from 0.13 to 0.57 and from 0.21 to 0.64, respectively. Cross-species amplification was tested in Pleurodeles nebulosus, which is listed as Vulnerable by the IUCN. Eight new and seven previously published loci amplified successfully in that species and thus represent a valuable conservation tool. The novel microsatellites will be useful for a better understanding of the population dynamics, demography, genetic structure, and evolutionary history of Pleurodeles waltl and P. nebulosus.

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A new set of microsatellite loci for Cattleya walkeriana Gardner, an endangered tropical orchid species and its transferability to Cattleya loddigesii Lindl. and Cattleya nobilior Reichenbach

Plant Genetic Resources ◽

10.1017/s1479262117000193 ◽

2017 ◽

Vol 16 (3) ◽

pp. 284-287

Author(s):

Bruno C. Rossini ◽

Mariá B. Kampa ◽

Celso L. Marino ◽

Fernanda Bortolanza Pereira ◽

Fábio M. Alves ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Loci ◽

Null Alleles ◽

Germplasm Resources ◽

Significant Linkage Disequilibrium ◽

Orchid Species ◽

Expected Heterozygosity ◽

Tropical Orchid ◽

Significant Linkage

AbstractIn this study, we isolate and analyse a new set of microsatellite loci for Cattleya walkeriana. Twenty-two primer pairs were screened for C. walkeriana (n = 32) and assessed for their transferability to Cattleya loddigesii (n = 12) and Cattleya nobilior (n = 06). All loci amplified for C. walkeriana; however, for C. loddigesii and C. nobilior, four and five primers, respectively, did not present amplification. The polymorphic loci presented between 2 and 13 alleles per locus for both C. walkeriana and C. loddigesii, with respective averages of 5.1 and 4.2. For C. nobilior, we found between two and five alleles per locus, with an average of 2.6. For C. walkeriana, observed heterozygosity varied from 0.100 to 0.966, whereas expected heterozygosity ranged from 0.097 to 0.900. The observed and expected heterozygosity for C. loddigesii and C. nobilior were also estimated. We found no significant linkage disequilibrium between any pair of loci, and evidence of null alleles at four loci (Cw16, Cw24, Cw30 and Cw31) for C. walkeriana. The combined power to exclude the first parent and combined non-exclusion probability of identity were 0.999 and 2.3 × 10−20, respectively. These new loci can be used in studies of germplasm resources, and assessments of genotypic and genetic diversity and population structure, thus improving the accuracy of such analyses and their applicability in the conservation and protection of these endangered species.

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Genome survey and identification of polymorphic microsatellites provide genomic information and molecular markers for the red crab Charybdis feriatus (Linnaeus, 1758) (Decapoda: Brachyura: Portunidae)

Journal of Crustacean Biology ◽

10.1093/jcbiol/ruz074 ◽

2019 ◽

Vol 40 (1) ◽

pp. 76-81 ◽

Cited By ~ 3

Author(s):

Shaobin Fang ◽

Renxie Wu ◽

Xi Shi ◽

Yin Zhang ◽

Mhd Ikhwanuddin ◽

...

Keyword(s):

Microsatellite Loci ◽

Gc Content ◽

Repeat Sequence ◽

Sequencing Platform ◽

Genome Survey ◽

Expected Heterozygosity ◽

Polymorphic Microsatellites ◽

Polymorphic Microsatellite ◽

Insight Into ◽

Illumina Sequencing Platform

Abstract We conducted a whole genome survey in the portunid crab Charybdis feriatus (Linnaeus, 1758) using Illumina sequencing platform and developed a set of polymorphic microsatellite loci. A total of 117.7 Gb of clean reads were generated, with 74× coverage of the estimated genome size of 1.4 Gb. The GC content, heterozygosity rate, and repeat sequence rate of the genome were estimated to be 40%, 1.1%, and 51%, respectively. A total of 3,779,209 microsatellites were identified from the genome. Sixty microsatellite loci were evaluated in a wild population of 40 individuals. As a result, 14 polymorphic microsatellite loci (23.3%) were obtained. The number of alleles (3 to 15), polymorphism information content (0.365 to 0.884), observed heterozygosity (0.050 to 0.975), and expected heterozygosity (0.450 to 0.907) per locus averaged 6.8, 0.652, 0.691, and 0.707, respectively. We show that the genome of C. feriatus has a high heterozygosity and repeat sequence rates, and provide a novel insight into the genome profile of marine crabs. The genetic markers developed in this study are potentially useful for studies on population dynamics and conservation genetics of C. feriatus and other species of brachyuran crabs.

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Deviation from Hardy–Weinberg equilibrium, and temporal instability in allele frequencies at microsatellite loci in a local population of Atlantic cod

ICES Journal of Marine Science ◽

10.1016/j.icesjms.2005.05.009 ◽

2005 ◽

Vol 62 (8) ◽

pp. 1588-1596 ◽

Cited By ~ 25

Author(s):

Sten Karlsson ◽

Jarle Mork

Keyword(s):

Microsatellite Loci ◽

Atlantic Cod ◽

Local Population ◽

Allele Frequencies ◽

Null Alleles ◽

P Value ◽

Patchy Distribution ◽

Hardy Weinberg Equilibrium ◽

The One ◽

Weinberg Expectation

Abstract A total of 1455 spawning cod, sampled from a local spawning area in Trondheimsfjord (Norway) between 1985 and 2002, was screened at the microsatellite loci Gmo132 and Gmo2. Samples from 15 spawning years comprising 29 consecutive cohorts were analysed. At the Gmo132 locus, but not at Gmo2, allele frequencies varied significantly among sampling years as well as cohorts, corresponding to FST-values of 0.004 and 0.006, respectively. Both loci showed examples of significant deviations from Hardy–Weinberg expectation within sampling years as well as cohorts, manifested as deficiencies of heterozygotes. Combining the p-values from the single tests (Fisher's method) revealed an overall significant p-value for deviation from the Hardy–Weinberg expectations at Gmo132 but not at Gmo2. Trend tests showed significant HW deficiencies at both loci for annual samples but not for cohorts. Possible reasons for the deficiencies were discussed; inter alia the existence of null alleles, or a form of pseudo Wahlund effect due to a patchy distribution of habitats for settling O-group cod in the Trondheimsfjord. It was noted that there might be a relationship between the relatively high temporal within-population variability of allele frequencies at Gmo132 and the fact that among microsatellite loci studied so far, Gmo132 is the one that usually shows the highest genetic differentiation geographically in cod.

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