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 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 and characterization of 26 novel microsatellite loci for the trochid gastropodGibbula divaricata(Linnaeus, 1758), using IlluminaMiSeqnext generation sequencing technology

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1789 ◽  
Author(s):  
Violeta López-Márquez ◽  
Ricardo García-Jiménez ◽  
José Templado ◽  
Annie Machordom
Keyword(s):  
Microsatellite Loci ◽  
High Throughput Sequencing ◽  
Illumina Miseq ◽  
Null Alleles ◽  
Sequencing Technology ◽  
Sympatric Distribution ◽  
Biogeographic Patterns ◽  
Hardy Weinberg Equilibrium ◽  
Significant Linkage

In the present study we used the high-throughput sequencing technology Illumina MiSeq to develop 26 polymorphic microsatellite loci for the marine snailGibbula divaricata. Four to 32 alleles were detected per locus across 30 samples analyzed. Observed and expected heterozygosities ranged from 0.130 to 0.933 and from 0.294 to 0.956, respectively. No significant linkage disequilibrium existed. Seven loci deviated from Hardy-Weinberg equilibrium that could not totally be explained by the presence of null alleles. Sympatric distribution with other species of the genusGibbula, asG. rarilineataandG. varia, lead us to test the cross utility of the developed markers in these two species, which could be useful to test common biogeographic patterns or potential hybridization phenomena, since morphological intermediate specimens were found.

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

2005 ◽  
Vol 62 (8) ◽  
pp. 1588-1596 ◽  
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.

Characterization of 17 novel microsatellite loci in the Nile monitor (Varanus niloticus) via 454 pyrosequencing

2016 ◽  
Vol 37 (1) ◽  
pp. 121-125 ◽  
Author(s):  
Jared P. Wood ◽  
Todd S. Campbell ◽  
Robert B. Page
Keyword(s):  
Microsatellite Loci ◽  
454 Pyrosequencing ◽  
Sequence Similarity ◽  
Null Alleles ◽  
The Us ◽  
Hardy Weinberg Equilibrium ◽  
The City ◽  
Two Populations ◽  
Genotypic Disequilibrium

We used 454 pyrosequencing to characterize 17 novel microsatellite loci from the Nile monitor (Varanus niloticus), using samples from an invasive population in the US state of Florida. These markers were screened for variation in 40 individuals from the City of Cape Coral. Observed heterozygosity ranged from 0.18 to 0.73 (mean ± SE = 0.46 ± 0.06) and the number of alleles per locus ranged from 1 to 4 (mean ± SE = 2.5 ± 0.2). Preliminary genotyping of samples from populations in West Palm Beach and Homestead revealed two loci (Mon6andMon15) that are monomorphic in Cape Coral, but polymorphic in these other two populations. We found no statistical departures from Hardy-Weinberg equilibrium or evidence of null alleles. However, there was statistical evidence for genotypic disequilibrium betweenMon1-Mon14andMon3-Mon8. BLASTn searches of NCBI’s nr/nt database identified four microsatellites containing 454 fragments that exhibit substantial sequence similarity to loci in other reptilian genomes, suggesting these markers should be prioritized by researchers interested in cross-amplification in other varanids. The resources we have developed will enable investigations of the population genetic dynamics of invasive Nile monitors in Florida and may facilitate studies within this species native range.

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.

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

2015 ◽  
Vol 36 (3) ◽  
pp. 318-324 ◽  
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.

scholarly journals Cross-Species Amplification of Microsatellite Loci for the Endangered Conifer, Taxus chinensis var. mairei (Taxaceae)

2012 ◽  
Vol 61 (1-6) ◽  
pp. 287-291 ◽  
Author(s):  
Y. Wen ◽  
K. Uchiyama ◽  
G. Xu ◽  
S. Ueno ◽  
W. Han ◽  
...  
Keyword(s):  
Endangered Species ◽  
Genetic Analysis ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Rare Species ◽  
Null Allele ◽  
Null Alleles ◽  
Taxus Chinensis ◽  
Congeneric Species ◽  
Expected Heterozygosity

AbstractBeing an economical and endangered species, microsatellite markers of Taxus chinensis var. mairei were very limited. We have developed a set of microsatellite markers, which was benefit for future genetic analysis of this rare species. Polymorphic loci were developed from congeneric species by cross-species amplification methods, and new primers were redesigned to test for potential null alleles. 15 loci showed polymorphism. The number of alleles per locus varied from 2 to 23 tested in 48 individuals. The observed heterozygosity (Ho) and expected heterozygosity (He) values ranged form 0.000 to 0.854 and 0.082 to 0.827, respectively. Newly redesigned primer confirmed that no null allele existed in most suspected loci. These microsatellite markers will be useful for future genetic analysis and conservation of this endangered species.

scholarly journals Isolation and Characterization of Polymorphic Microsatellite Markers for Two Subterranean Termites

Sociobiology ◽  
2017 ◽  
Vol 64 (3) ◽  
pp. 352 ◽  
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.

scholarly journals Isolation and Characterization of Microsatellite Markers for Soybean Looper (Lepidoptera: Noctuidae)

2019 ◽  
Vol 19 (5) ◽  
Author(s):  
C S Silva ◽  
E M G Cordeiro ◽  
A S Corrêa
Keyword(s):  
Population Structure ◽  
Microsatellite Markers ◽  
Null Alleles ◽  
Isolation And Characterization ◽  
Hardy Weinberg Equilibrium ◽  
High Degree ◽  
Soybean Looper ◽  
Lepidoptera Noctuidae ◽  
F Statistics

Abstract We constructed 13 microsatellite markers for Chrysodeixis includens (Walker), a serious crop pest in the Americas. All SSR (Simple Sequence Repeat) markers were polymorphic, with no evidence of linkage disequilibrium between any loci in any population. The total number of alleles per locus ranged from 5 for L3, L9, and L11 to 26 for L6; the mean number of alleles per locus in three populations of C. includens ranged from 2.33 for L3 to 14.67 for L6. Hardy–Weinberg equilibrium (HWE) deviation was not observed in four loci for at least one population (L3, L5, L9, L10). Markers L6, L7, L8, L10, L11, L12, and L13 showed a frequency of null alleles > 0.2 for at least one population. STRUCTURE and F-statistics revealed low population structure among the populations (FST = 0.013) and a high degree of inbreeding (FIS = 0.658). The SSR markers developed here will be useful in future studies on the ecology, demography, host dynamics, and gene flow of C. includens. This information is essential to understand the recent status of C. includens as a key pest in South America.

Genetic Characterization of Indigenous Duck of North-East Region using Microsatellite Markers

2021 ◽  
Author(s):  
Purabi Kaushik ◽  
Jnyanashree Saikia ◽  
Kabitabala Kalita ◽  
Rajjyoti Deka ◽  
J. Saharia
Keyword(s):  
Microsatellite Markers ◽  
Genetic Characterization ◽  
The Other ◽  
North East India ◽  
North East ◽  
Brahmaputra Valley ◽  
East Region ◽  
Hardy Weinberg Equilibrium ◽  
Common Variety

Background: Duck farming plays a significant role, next to chicken in the socio-economic uplift men of the rural farmers of North-East India. Pati duck is the most common duck breed in the Brahmaputra valley of Assam and the other common variety reared in North-East India is Chara-Chambeli, however it originatein Kerala. Genetic characterization plays a significant role for formulation of breeding strategies for improvement of any breed. Microsatellites are codominant in nature and are highly polymorphic. High level of allelic variation, co-dominant mode of inheritance and potential for automated analysis make them an excellent tool for genotyping, mapping and genetic characterization. Pati duck is the most common duck breed in the Brahmaputra valley of Assam and the other common variety reared in North-East India is Chara-Chambeli however its origin in Kerela. Therefore, the present investigation was carried out to characterize these two duck breeds using microsatellite markers to evaluate the genetic diversity in these two duck population. Methods: For the present study, Blood sample were collected from 50 Patiducks and 50 Chara-Chambeli ducks from different parts of North-East India. Assessment of genetic characterization of duck breeds of north-east region were carried out using 16 microsatellite markers and population genetics analysis were done by POPGENE software. Result: In the present study, all the studied loci were highly polymorphic. Analysis generated a total of 41 microsatellite alleles. The number of observed alleles (Na) with an overall mean of 1.93±0.258. However, the effective number of alleles (Ne) with a mean of 1.6933±0.2712. The Shannon’s information index was found to a mean value of 0.5685±0.1693. The overall means for observed (HO) and expected (He) heterozygosities were 0.2889±0.2477 and 0.5289±0.0853, respectively. The chi-square (χ2) test for Hardy-Weinberg equilibrium revealed that all the loci are in within Hardy-Weinberg equilibrium.

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