scholarly journals ISOLATION AND CHARACTERIZATION OF NEW MICROSATELLITE MARKERS FOR THE CORTÉS GEODUCK (Panopea globosa)

2016 ◽  
Vol 31 (1) ◽  
pp. 17
Author(s):  
Celia Isabel Bisbal -Pardo ◽  
Miguel Ángel Del Río -Portilla ◽  
Ana Yonori Castillo -Paéz ◽  
Axayácatl Rocha-Olivares
Keyword(s):  
Fishery Management ◽  
Genetic Research ◽  
Isolation And Characterization ◽  
Expected Heterozygosity ◽  
Tetranucleotide Repeats ◽  
Hardy Weinberg Equilibrium ◽  
Increasing Demand ◽  
Sustainable Fishery ◽  
Generation Technology

The geoduck Panopea globosa is a long-lived and large endemic infaunal clam sustaining a growing fishery in the Northwest coast of México that, in spite of its increasing demand in Asian markets very little is known about its biology. In order to provide genetic markers to support genetic research of wild populations, nine novel microsatellite loci (di-, tri-, and tetranucleotide repeats) were developed using shotgun sequencing with next generation technology (Illumina). The number of alleles per locus ranged from 3 to 16 and the observed and expected heterozygosity ranged from 0.286 to 0.650 and 0.504 to 0.906, respectively. Five loci were found to be significantly deviated from the Hardy-Weinberg equilibrium and three pairs showed evidence of linkage disequilibrium. Most loci are highly informative for population genetics and linkage analyses according to their polymorphism information content (> 0.5) and will be useful for increasing our understanding of the wild population structure and developing a sustainable fishery management. Aislamiento y caracterización de nuevos marcadores microsatelitales en la almeja generosa (Panopea globosa) La almeja generosa Panopea globosa es una especie infáunica longeva y de gran tamaño que mantiene una pesquería creciente en la costa del Noroeste de México. A pesar de su demanda creciente en los mercados asiáticos, se conoce muy poco acerca de su biología. Con la finalidad de proveer nuevos marcadores genéticos para la caracterización de poblaciones silvestres, se desarrollaron nueve marcadores microsatelitales nuevos (con patrones repetidos de di-, tri-, y tetranucleotídicos) utilizando secuenciación genómica aleatoria con tecnología de secuenciación de siguiente generación (Illumina). El número de alelos por locus varió de 3 a 16 y los valores de heterocigosidad observada y esperada variaron de 0.286 a 0.650 y 0.504 a 0.906, respectivamente. Cinco microsatelites se desvían del equilibrio de Hardy-Weinberg y tres pares de microsatélites mostraron evidencia de desequilibrio de ligamiento. La mayoría de los loci son altamente informativos para estudios poblacionales y análisis de ligamiento de acuerdo con su contenido de información de polimorfismos (> 0.5) y serán útiles para incrementar el conocimiento de la estructura genética de las poblaciones silvestres de esta almeja y para coadyuvar en su pesquería sustentable.

scholarly journals Development and Characterization of 135 SNP Markers in Chiton Acanthochitona Rubrolineatus

2021 ◽  
Author(s):  
Jirui zhang ◽  
Yunqi Song ◽  
Chenghong Wang ◽  
Shukui Zhang ◽  
Zilin Jiang ◽  
...  
Keyword(s):  
Snp Markers ◽  
Wild Populations ◽  
Effective Protection ◽  
Population Genetic Analysis ◽  
Important Species ◽  
Polymorphic Snps ◽  
Isolation And Characterization ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium

Abstract Acanthochitona rubrolineatus (Lischke, 1873) (Polyplacophora, Neoloricata, Cryptoplacidae) is an important species widely distributed in the middle and low tide zone of coastal intertidal zone along the China Sea coast. In recent years, the serious pollution of seawater has caused a sharp decline in the number of wild populations of A. rubrolineatus. Lacking of effective molecular markers limits the effective protection and management of this species. Studies for the isolation and characterization of 135 A. rubrolineatus SNPs markers were carried out. The frequency of minor allele ranges from 0.0125 to 0.5000. The observed heterozygosity and expected heterozygosity are 0.0000-0.9750, 0.0731-0.6696, respectively. The inbreeding value varies from -0.2902 to 0.9966. Among them, there are 27 sites markablely differently from Hardy-Weinberg equilibrium (P < 0.05). The study of the polymorphic SNPs will provide a therotical basis for further analysis of population genetic analysis on A. rubrolineatus.

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 Loci for the Ornamental Plant Primula obconica Hance (Primulaceae)

HortScience ◽  
2010 ◽  
Vol 45 (2) ◽  
pp. 314-315 ◽  
Author(s):  
Hai-fei Yan ◽  
Xue-jun Ge ◽  
Chi-ming Hu ◽  
Gang Hao
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Ornamental Plant ◽  
Microsatellite Variation ◽  
Isolation And Characterization ◽  
Expected Heterozygosity ◽  
Fiasco Protocol

Nine microsatellite loci were isolated from Primula obconica using the FIASCO protocol. We used 30 individuals from three populations for the assessment of microsatellite variation. Seven loci were detected with microsatellite polymorphism. The number of alleles per locus ranged from three to seven. The average observed heterozygosity and expected heterozygosity ranged from 0.167 to 0.6 and from 0.409 to 0.653, respectively. These microsatellite markers will be useful to assess the genetic variation and genetic structure of P. obconica.

scholarly journals Isolation and Characterization of Polymorphic Microsatellite loci from the Invasive Worm Branchiomma luctuosum (Grube, 1870) (Annelida: Sabellidae)

2018 ◽  
Author(s):  
Flávia Ariany Belato ◽  
Elisa Maria Costa-Paiva ◽  
Paulo Cesar Paiva ◽  
Anderson Vilasboa
Keyword(s):  
Null Alleles ◽  
Anthropogenic Activity ◽  
Brazilian Coast ◽  
Isolation And Characterization ◽  
History Of ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
High Level ◽  
Activity Areas

Introduction of exotic species in new areas through anthropic action is one of the major problems that can affect biodiversity. Branchiomma luctuosum is known for its highly invasive potential and the actual occurrence of species commonly associated with port activity areas is an extra evidence that this anthropogenic activity should not be underestimated. In order to develop suitable molecular markers for future studies on colonization routes and population dynamics of the invading individuals of B. luctuosum, nine highly polymorphic microsatellite loci were isolated and their polymorphism levels were evaluated. These loci showed a range of number of alleles per locus from five to ten and all loci had a high level of genetic diversity, and exhibited significant heterozygote deficiencies probably due to the presence of null alleles. Significant deviations from the Hardy-Weinberg equilibrium were detected at several loci and most of them were related to a heterozygous deficit. Heterozygous deficiency can be expected in this case due to the biology and history of this invasive species, in relation to its recent introduction in Brazilian coast and possible action of multiple introductory events.

scholarly journals Isolation And Characterization Of 45 SNP Markers In Triplophysa Tenuis

2021 ◽  
Author(s):  
Ya Liu ◽  
Yeyu Chen ◽  
Jiansheng Lai ◽  
Hongyu Ke ◽  
Zhongmeng Zhao ◽  
...  
Keyword(s):  
Polymorphic Information Content ◽  
Snp Markers ◽  
Gansu Province ◽  
The Novel ◽  
Genetic Management ◽  
Polymorphic Snps ◽  
Isolation And Characterization ◽  
Population Conservation ◽  
Hardy Weinberg Equilibrium

Abstract Triplophysa tenuis is an endemic species to China, which mainly distributed in Xinjiang and Gansu province. Effective conservation and management of this species is limited by insufficient molecular markers. In the present study, we reported the isolation and characterization of 45 SNP markers in T. tenuis. The minor allele frequency ranged from 0.046 to 0.500, and the observed and expected heterozygosities ranged from 0.061 to 0.667 and 0.088 to 0.508, respectively. Polymorphic information content ranged from 0.083 to 0.375. Among these SNPs, three loci showed significant departures from the Hardy–Weinberg equilibrium. The novel polymorphic SNPs will be helpful for the future study on genetic management and population conservation for this species.

scholarly journals Characterization of Single Nucleotide Polymorphism Marker in the Chinese Giant Salamander Andrias davidianus

2021 ◽  
Author(s):  
Quanhe Wang ◽  
Lei Cheng ◽  
Haifeng Tian ◽  
Xiaoli Dong ◽  
Hanbing Xiao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Nutritional Value ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Andrias Davidianus ◽  
Allele Number ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium ◽  
Chinese Giant Salamander

Background: Chinese giant salamander Andrias davidianus is called “baby fish” in China. Due to its palatability and nutritional value, it was widely cultured in China. The current study was to evaluate the genetic diversity of the farmed A. davidianus. Methods: 30 salamanders were collected from farm and DNA was extracted. Thirty contigs potentially containing SNPs were selected from the previously developed RAD-seq library. The primer was designed and PCR was performed, than the products was sequenced from different direction. At last the sequences were analyzed using the vector NTI 10.Result: 5824bp high-quality sequences embodied in 16 contigs were sequenced and eighty SNP loci were identified which each SNP locus exhibited bi-alleles. The effective allele number from 1.03 to 2.00 and the minor allele frequency was 0.017 to 0.500. The expected heterozygosity was from 0.0333 to 0.5091 and the observed heterozygosity was 0.0333 to 1.0000. Sixty-six of the 80 loci significantly deviated from the Hardy-Weinberg equilibrium (P less than 0.05). The results provide useful genomic resources to evaluate the genetic diversity of A. davidianus for conservation and aquaculture.

scholarly journals Isolation and Characterization of Polymorphic Microsatellite loci from the Invasive Worm Branchiomma luctuosum (Grube, 1870) (Annelida: Sabellidae)

2018 ◽  
Author(s):  
Flávia Ariany Belato ◽  
Elisa Costa-Paiva ◽  
Anderson Vilasboa
Keyword(s):  
Null Alleles ◽  
Anthropogenic Activity ◽  
Brazilian Coast ◽  
Isolation And Characterization ◽  
History Of ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
High Level ◽  
Activity Areas

Introduction of exotic species in new areas through anthropic action is one of the major problems that can affect biodiversity. Branchiomma luctuosum is known for its highly invasive potential and the actual occurrence of species commonly associated with port activity areas is an extra evidence that this anthropogenic activity should not be underestimated. In order to develop suitable molecular markers for future studies on colonization routes and population dynamics of the invading individuals of B. luctuosum, nine highly polymorphic microsatellite loci were isolated and their polymorphism levels were evaluated. These loci showed a range of number of alleles per locus from five to ten and all loci had a high level of genetic diversity, and exhibited significant heterozygote deficiencies probably due to the presence of null alleles. Significant deviations from the Hardy-Weinberg equilibrium were detected at several loci and most of them were related to a heterozygous deficit. Heterozygous deficiency can be expected in this case due to the biology and history of this invasive species, in relation to its recent introduction in Brazilian coast and possible action of multiple introductory events.

scholarly journals Isolation and Characterization of 10 Polymorphic Microsatellite Loci in Paphiopedilum concolor (Batem.) Pfitzer (Orchidaceae) and Cross-species Amplification

HortScience ◽  
2010 ◽  
Vol 45 (8) ◽  
pp. 1286-1287 ◽  
Author(s):  
Long-na Li ◽  
Songjun Zeng ◽  
Feng Zheng ◽  
Zhi-lin Chen ◽  
Kun-lin Wu ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Microsatellite Locus ◽  
Microsatellite Loci ◽  
Genomic Library ◽  
Enriched Genomic Library ◽  
Relationship Patterns ◽  
Isolation And Characterization ◽  
Expected Heterozygosity ◽  
Polymorphic Microsatellite

Ten polymorphic microsatellite loci were isolated and characterized from an enriched genomic library of Paphiopedilum concolor (Batem.) Pfitzer. The number of alleles per microsatellite locus ranged from three to 11 with an average of 6.4 in a sample of 30 individuals from three populations. The observed and expected heterozygosity ranged from 0.200 to 0.800 and from 0.544 to 0.827, respectively. These microsatellites can be used as tools to investigate the genetic structure of P. concolor populations and relationship patterns with closely related taxa.

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 Isolation and Characterization of Fifteen Microsatellite Loci for the Use in Breeding of Gmelina arborea Roxb. (Lamiaceae)

2020 ◽  
Vol 1 (2) ◽  
pp. 23-28
Author(s):  
Oscar Rocha ◽  
Dawa Méndez-Álvarez ◽  
Fabiana Rojas Parajeles ◽  
Olman Murillo Gamboa
Keyword(s):  
Microsatellite Loci ◽  
Clonal Selection ◽  
Gmelina Arborea ◽  
Pairwise Similarity ◽  
Isolation And Characterization ◽  
Tropical Areas ◽  
Hardy Weinberg Equilibrium ◽  
Shared Alleles ◽  
Adequate Management

Gmelina arborea (melina) is a valuable tree species throughout tropical areas, and there are extensive commercial plantations of this species in Southeast Asia, West Africa, and Latin America. As part of a research program for the genetic improvement and management of G. arborea at Instituto Tecn´ologico de Costa Rica, we developed, validated, and optimized fifteen microsatellite loci. We used 23 clones belonging to five different companies currently using clonal selection to manage their commercial plantations. Our results showed that all fifteen loci were polymorphic and together had 75 alleles (2-7 alleles/locus). We also found that eleven loci showed lower heterozygosity than expected under Hardy-Weinberg equilibrium (HWE). We calculated the genetic similarity among all clone pairs using the number of shared alleles to examine the potential of these loci for clone discrimination. Overall, pairwise similarity among clones ranged from 0.36 to 0.83, and our findings also showed that clones from the same commercial plantation tended to be more similar to each other than to clones from other plantations. These microsatellite loci will contribute toward the characterization of the genetic diversity, the identification of elite clone lines for timber production, and breeding and adequate management of commercial plantations of G. arborea.

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