Characterization of novel microsatellite markers forHyphantria cuneaand implications for other Lepidoptera

2015 ◽  
Vol 105 (3) ◽  
pp. 273-284 ◽  
Author(s):  
L.J. Cao ◽  
J.B. Wen ◽  
S.J. Wei ◽  
J. Liu ◽  
F. Yang ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Asian Countries ◽  
Hyphantria Cunea ◽  
Genetic Studies ◽  
Hardy Weinberg Equilibrium ◽  
Mutation Pattern ◽  
Significant Linkage ◽  
Simple Sequence ◽  
Better Than

AbstractThis is the first report of microsatellite markers (simple sequence repeats, SSR) for fall webworm,Hyphantria cunea(Drury) (Lepidoptera: Arctiidae), an important quarantine pest in some European and Asian countries. Here, we developed 48 microsatellite markers forH. cuneafrom SSR enrichment libraries. Sequences isolated from libraries were sorted into four categories and analyzed. Our results suggest that sequences classified asGroupedshould not be used for microsatellite primer design. The genetic diversity of microsatellite loci was assessed in 72 individuals from three populations. The number of alleles per locus ranged from 2 to 5 with an average of 3. The observed and expected heterozygosities of loci ranged from 0 to 0.958 and 0 to 0.773, respectively. A total of 18 out of 153 locus/population combinations deviated significantly from Hardy–Weinberg equilibrium. Moreover, significant linkage disequilibrium was detected in one pair of loci (1275 pairs in total). In the neutral test, two loci were grouped into the candidate category for positive selection and the remainder into the neutral category. In addition, a complex mutation pattern was observed for these loci, andFSTperformed better than didRSTfor the estimation of population differentiation in different mutation patterns. The results of the present study can be used for population genetic studies ofH. cunea.

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 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.

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.

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 Parental contribution in a cultivated stock for the spotted rose snapper Lutjanus guttatus (Steindachner, 1869) estimated by newly developed microsatellite markers

2020 ◽  
Vol 48 (2) ◽  
pp. 247-256
Author(s):  
Ricardo Perez-Enriquez ◽  
Janeth A. Valadez-Rodríguez ◽  
Adriana Max-Aguilar ◽  
Silvie Dumas ◽  
Noé Diaz-Viloria
Keyword(s):  
Wild Population ◽  
Management Strategies ◽  
Population Sample ◽  
Genetic Studies ◽  
Hardy Weinberg Equilibrium ◽  
Parental Couple ◽  
Cultivated Populations ◽  
Species Specific ◽  
Generation Sequencing

The spotted rose snapper Lutjanus guttatus is a fishery relevant species from the eastern Pacific Ocean, with aquaculture potential. Species-specific genetic markers are needed for the genetic characterization of wild and cultivated populations to help management strategies. Eighteen hypervariable microsatellites were developed by Next Generation Sequencing and characterized in a wild population sample. Genetic diversity was high (observed heterozygosity = 0.88 ± 0.050; the number of alleles per locus = 13.4 ± 1.3) and few loci departed from the Hardy-Weinberg Equilibrium, leaving 14 loci potentially suitable for population genetic studies. A reduced panel of five loci was tested in a cultivated stock to determine the parentage of progeny (embryonated eggs; n = 413), to estimate the temporal contribution of each parental broodstock. The above resulted in the successful assignment of 95.6% of the progeny to its parental couple, representing 17 out of the 24 possible families. Two of the four females produced most of those progeny (97.3%). These females, which reproduced throughout the season, did not spawn on consecutive days. The contribution of males was evenly distributed during the season and occurred on successive days. Some microsatellites can be used in other lutjanids (L. peru, L. argentiventris, and Hoplopagrus guentherii).

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 Characterization of simple sequence repeat loci for Peltigera membranacea (lichenized Ascomycota) and its Nostoc photobiont

2021 ◽  
Vol 53 (6) ◽  
pp. 457-465
Author(s):  
Silke Werth ◽  
Stefán Þór Pálsson ◽  
Ólafur S. Andrésson
Keyword(s):  
Simple Sequence Repeat ◽  
Population Genetic ◽  
Common Ground ◽  
Gene Diversity ◽  
Similar Species ◽  
Sequence Repeat ◽  
Genetic Studies ◽  
Unbiased Gene ◽  
Simple Sequence

AbstractTo facilitate population-genetic studies, we developed simple sequence repeat (SSR) markers and a molecular species identification assay for Peltigera membranacea (Ascomycota, Peltigerales), a common ground-dwelling lichen of forest and tundra ecosystems. Additional markers were developed for its Nostoc photobiont. Twenty-one fungal markers for P. membranacea were found to be polymorphic, with the number of alleles ranging from 3–21. Nei's unbiased gene diversity ranged from 0.588 to 0.640 in four significantly structured (FST = 0.059) mycobiont populations. For the Nostoc photobiont, 14 polymorphic SSR were developed, yielding 4–14 alleles each, with gene diversity ranging from 0.062 to 0.771 in four populations showing substantial population structure (FST = 0.278). The new markers developed are suitable for population genetic studies of Peltigera membranacea and of its cyanobiont, and at the same time allowed us to distinguish 98.5% of P. membranacea specimens from morphologically similar species of Peltigera.

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.

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