Characterization Of Microsatellite DNA Markers Research Articles

Isolation and Characterization of Microsatellite DNA Markers in the Deep-Sea Amphipod Paralicella tenuipes by Illumina MiSeq Sequencing.

Here, we describe the development of 16 polymorphic microsatellite markers using an Illumina MiSeq sequencing approach in the deep-sea amphipod Paralicella tenuipes A total of 25 577 844 DNA sequences were filtered for microsatellite motifs of which 197 873 sequences were identified. From these sequences, 64 had sufficient flanking regions for primer design and 16 of these loci were polymorphic. Between 5 and 30 alleles were detected per locus, with an average of 13.63 alleles per locus, across a total of 120 individuals from 5 separate deep sea trenches from the Pacific Ocean. For the 16 loci, observed and expected heterozygosity values ranged from 0.116 to 0.414 and 0.422 to 0.820, respectively, with one locus displaying significant deviation from Hardy-Weinberg equilibrium. The microsatellite loci that have been isolated and described here are the first molecular markers developed for deep sea amphipods and will be invaluable for elucidating the genetic population structure and the extent of connectivity between deep ocean trenches.

Isolation and characterization of microsatellite DNA markers in the Greater Roadrunner (Geococcyx californianus)

We report the development of eight polymorphic microsatellite loci for the Greater Roadrunner (Geococcyx californianus), a terrestrial cuckoo distributed in the US Southwest and Mexico. These markers will be useful for population genetics and molecular ecology studies of this bird.

Isolation and Characterization of Microsatellite DNA Markers for the Oriental White Stork,Ciconia boyciana

Following FIASCO protocol and across-amplification approach, we present eleven microsatellite primers of the Oriental White stork, Ciconia boyciana in this article. All loci were polymorphic, except for locus Cbo235, which possessed two alleles but was homozygous in all 23 individuals of C. boyciana used in this study. The number of the alleles per locus ranged from two to eight, and the observed heterozygosity (H(o)) and expected heterozygosity (H(E)) ranged from 0 to 0.857 and 0.222 to 0.851, respectively. These markers are proved useful in genetic study of C. boyciana.

Isolation and characterization of microsatellite DNA markers in the critically endangered St. Croix ground lizard Ameiva polops

We report the development of nine polymorphic microsatellite loci for the critically endangered St. Croix ground lizard Ameiva polops. These loci will be useful to determine the genetic health of extant populations of this lizard and their levels of genetic differentiation.

Microsatellite DNA markers for comparative phylogeography analysis in the Korean field mouse (Apodemus peninsulae) and large-eared field mouse (Apodemus latronum)

The sympatric Apodemus species are excellent models for studying comparative phylogeography of organisms. On basis of the microsatellite development of three Apodemus species, we describe in this paper the isolation and characterization of microsatellite DNA markers in the two Apodemus species (Apodemus peninsulae and Apodemus latronum) from genomic DNA-enriched libraries. Ten and eight polymorphic loci were found in A. peninsulae and A. latronum, respectively. These loci were highly polymorphic with numbers of alleles per locus ranging from 11–20 and 6–16, and expected heterozygosity from 0.891–0.947 and 0.714–0.950 for A. peninsulae and A. latronum, respectively. Seven and six loci followed Hardy–Weinberg expectations for A. peninsulae and A. latronum, respectively. No significant linkage association was found among all these loci. These polymorphic microsatellite loci will be useful in studying comparative phylogeography of the sympatric Apodemus species.

Isolation and characterization of microsatellite DNA markers for the flagfish Jordanella floridae

The flagfish (Jordanella floridae) is commonly used in studies of wetlands ecology. Here we describe the isolation of ten microsatellite loci, six of which were polymorphic. The observed number of alleles ranged from 4 to 24 and observed heterozygosities ranged from 0.59 to 0.81 for the polymorphic loci. The isolation of these markers will enable estimations of genetic diversity in natural populations.

Development and characterization of microsatellite DNA markers for the Alpine plant species Campanula thyrsoides

AbstractWe isolated and characterized eight polymorphic microsatellite markers for the Alpine plant species Campanula thyrsoides (Campanulaceae). Number of alleles per locus ranged from six to 12 and the observed heterozygosity was between 0.529 and 0.900. Observed vs. expected heterozygote deficits were significantly different in one out of eight loci following Bonferroni's correction for multiple tests. We did not find evidence for linkage disequilibrium between locus pairs. The microsatellite markers are being used for the study of genetic variation and gene flow within and among populations of C. thyrsoides in the Swiss Alps.

Characterization of microsatellite DNA markers for a mahseer species, Tor tambroides (Cyprinidae) and cross‐amplification in four congeners

AbstractThis study reports the isolation and characterization of microsatellite DNA markers in a mahseer species, Tor tambroides (Pisces, Cyprinidae). Of a total of 14 loci evaluated, 10 were polymorphic in T. tambroides samples, with an average of 2.86 alleles per locus. Deviations from Hardy–Weinberg equilibrium were observed at one locus and there was no indication of linkage disequilibrium among loci. A high level of cross‐amplification among four congeners was achieved, with 12 loci successfully amplifying and 11 loci showing polymorphism in at least one other species. These markers will be a useful resource for population genetic studies and broodstock management of closely related mahseer species.

Isolation and characterization of microsatellite DNA markers in endangered Mekong giant catfish Pangasianodon gigas

The Mekong giant catfish is one of the largest freshwater fish in the world, and is endemic to the Mekong basin. Recently, the number of Mekong giant catfish has drastically decreased. In this study, seven microsatellite DNA markers of the Mekong giant catfish were developed for evaluation of the species’ genetic diversity. Mendelian inheritance of four of seven markers was confirmed using offspring (F1) produced from one pair. Number of alleles per locus in the founder population ranged 1–4 with a mean of 2.8, and that in F1 ranged 1–2 with a mean of 1.6. The expected heterozygosity in the founder population ranged 0–0.66 with a mean of 0.38, and that in F1 ranged 0–0.5 with a mean of 0.28. The mean expected heterozygosity in the founder population is apparently lower than that in Pangasius bocourti and other freshwater species, but higher than that in endangered species. In the future, the microsatellite data in this study will be used in minimal kinship approaches, because these individuals constitute the basic seed for release into wild in an effort to conserve the native population of Mekong giant catfish.

Characterization of microsatellite DNA markers in a critically endangered species, Mekong giant catfish, Pangasianodon gigas

AbstractMicrosatellite DNA markers for a critically endangered Mekong giant catfish (Pangasianodon gigas Roberts and Vidthayanon, 1991) were developed from fin clips collected from captive fish using (GT)15 probe. The number of alleles per locus ranged from two to four. The expected heterozygosities ranged from 0.13 to 0.68. Also, these primers were successfully amplified in four closely related species, Pangasius bocourti, Pangasius conchophilus, Pangasius larnaudii and Pangasius sanitwongsei with the number of alleles per locus ranged from 1 to 13, 1 to 16, 1 to 12 and 1 to 4, respectively. These markers should prove to be very useful for the evaluation of genetic diversity for this species and other related Pangasius species.

Isolation and characterization of microsatellite DNA markers in the Pacific abalone, Haliotis discus hannai

AbstractWe developed 17 new microsatellite markers in Haliotis discus hannai. All loci were found to be polymorphic with an average of 13.1 alleles per locus (range 3–28). The mean observed and expected heterozygosities were 0.77 (range 0.17–1.00) and 0.79 (range 0.42–0.96), respectively. Six loci deviated significantly from Hardy–Weinberg proportions, and thus should be used with caution. The high variabilities revealed in this study suggest that these microsatellite loci should provide useful markers for studies of trait mapping, kinship and population genetics.

Isolation and characterization of microsatellite DNA markers from mangrove crab, Scylla paramamosain

AbstractThe first five variable microsatellite DNA loci for mangrove crab, Scylla paramanosain, were developed. Allelic variation and other characteristics at these loci were examined in this species captured at the Urado Bay, Japan. The number of alleles per locus ranged from 24 to 44. The expected heterozygosity across loci ranged from 0.900 to 0.999 and probability of identity (PI) ranged from 2.8 × 10−3 to 1.7 × 10−2. Therefore, these microsatellite markers could be useful for estimating effect of stock enhancement release and population genetic structure of mangrove crab.

Isolation and characterization of microsatellite DNA markers in the grass Poa alpina L.

AbstractThe important fodder grass Poa alpina L. occurs at several ploidy levels with common aneuploidy. We isolated and characterized five polymorphic microsatellite markers for the study of molecular genetic variation of this species. As first examples of the value of the developed markers for population genetic analyses, we show that plants with more chromosomes have more microsatellite bands and that isolation by distance plays a small role in shaping microsatellite diversity of P. alpina in the Swiss Alps.

Identification and characterization of microsatellite DNA markers developed in an endangered cyprinid of the Mekong River, the seven‐line barb (Probarbus jullieni Sauvage, 1880)

AbstractMicrosatellite markers for an endangered cyprinid species of the Mekong River, the seven‐line barb (Probarbus jullieni Sauvage, 1880) were developed from the wild caught samples using (GT)15 probe. The number of alleles per locus ranged from seven to 16. The expected heterozygosities ranged from 0.47 to 0.91. Also, these primers were successfully amplified in the two closely related species, P. labeamajor and P. labeaminor. These markers have proven to be very useful for the population genetic structure study in this species and other related cyprinids.

Identification and characterization of microsatellite DNA markers developed in ide Leuciscus idus and Siberian roach Rutilus rutilus

AbstractThe first five microsatellite markers for the ide, Leuciscus idus, and four microsatellite markers for the Siberian roach, Rutilus rutilus, were designed. Cross‐amplification of ide markers was examined in Siberian roach and vice versa. The number of alleles per locus ranged from three to 13 in ide and from two to eight in roach. The expected heterozygosity ranged from 0.313 to 0.909 in ide and from 0.119 to 0.775 in roach. These markers could be used to evaluate the genetic population structure of these species and other fish from the Cyprinidae family.

Isolation and characterization of microsatellite DNA markers in the rare species barfin flounder (Verasper moseri) and its closely related species spotted halibut (V. variegatus)

AbstractBarfin flounder and spotted halibut have been selected in Japan as target species for stock enhancement due to the fact that the number of individuals of these species in the wild has been decreasing in the last three decades. Barfin flounder is now considered to be a rare species as its situation is critical. The first microsatellite DNA markers for barfin flounder and spotted halibut are described in this study. Cross‐amplification of barfin flounder markers was examined in spotted halibut species and vice versa.

Isolation and characterization of microsatellite DNA markers from the Lanyu scops owl (Otus elegans botelensis)

AbstractFrom a genomic library enriched for GATA/CTAT and GAAA/CTTT repeats, 12 polymorphic microsatellite markers were developed for the Lanyu scops owl (Otus elegans botelensis). Polymorphism of these loci was evaluated in a sample of 58 adult individuals of unknown relationship. The allele numbers of each locus were from five to 25 and the observed heterozygosity of each locus ranges from 0.707 to 0.914. When using these loci in parentage assignment, the probability of false parent exclusion is greater than 0.999. All loci conformed to Hardy–Weinberg expectations.

Isolation and characterization of microsatellite DNA markers in the malaria vector Anopheles maculipennis

AbstractThe Anopheles maculipennis complex includes the most important malaria vectors of the western Palearctic. Anopheles maculipennis s.s., one member of this complex, is a reported vector in the Middle East. Here we describe the isolation of 15 microsatellite polymorphic loci from the An. maculipennis s.s. genome, displaying a high among individual diversity (0.37–0.77) in a sample from France. Three loci displayed a significant departure from Hardy–Weinberg proportions, suggesting a substantial frequency of null alleles. The remaining 12 loci are good candidates for further genetic studies in this species.

Isolation and characterization of microsatellite DNA markers in the malaria vector Anopheles nili

AbstractThe mosquito Anopheles nili is widespread across tropical Africa and appears to be the major vector of malaria in some rural forested areas of central Africa. Here we describe the isolation of 11 microsatellite polymorphic loci from the A. nili genome, displaying a high among‐individual diversity (0.58–0.96) in samples from west Africa. Two loci displayed a significant departure from Hardy–Weinberg proportions across all samples, suggesting a substantial frequency of null alleles. The remaining nine loci are good candidates for further genetic studies in this species.

Isolation and characterization of microsatellite DNA markers in the malaria vector Anopheles sacharovi

AbstractThe mosquito Anopheles sacharovi, a member of the A. maculipennis complex, is an important malaria vector in the Middle East. Here we describe the isolation of 15 microsatellite polymorphic loci from the A. sacharovi genome, displaying a high among‐individual diversity (0.30–0.92) in a sample from Turkey. Seven loci displayed a significant departure from Hardy–Weinberg proportions, suggesting a substantial frequency of null alleles. The remaining eight loci are good candidates for further genetic studies in this species.