• Korean Journal of Ichthyology
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• v.32 no.2
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• pp.39-48
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• 2020

The slender shinner (Pseudopungtungia tenuicorpa), a tiny freshwater fish of about 8 to 10 cm belonging to Cyprinidae, is an endangered species found only in the Han and Imjin Rivers on the Korean Peninsula. During the breeding season, this species spawns in nests of Coreoperca herzi, a predator of this species, or small crevices on rocks. This unique reproductive ecology can make this species more vulnerable to anthropogenic perturbance that can further limit the places to spawn. Here, mtDNA and microsatellite loci were analyzed to identify the genetic diversity and structure of slender shinners and further to provide the basic data necessary for the conservation planning of this species. A total of 28 polymorphic microsatellite markers were developed using Illumina paired-end sequencing, and 67 slender shinners collected from three localities in the Han River were genotyped using these loci. This species showed a remarkably high level of genetic diversity with mean expected heterozygosity of 0.914 and mean allele number per locus of 27.9, and no signature of drastic demographic decline was detected. As a result of our microsatellite analysis, the genetic structure between the two stems of the Han River, North Han and South Han, was prominent. Such a genetic structure was also evident in the sequence analysis of 14 haplotypes obtained from mtDNA control region. Although slender shinners are only found in very limited areas around the world, the genetic structure indicates that there is a block of gene flow among the populations, which should be reviewed in the future if management and restoration of this species is needed.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.6
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• pp.888-901
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• 2020

Objective: A set of microsatellite markers with high polymorphism from Tsaiya duck were used for the genetic monitoring and genetic structure analysis of Brown and White Tsaiya duck populations in Taiwan. Methods: The synthetic short tandem repeated probes were used to isolate new microsatellite markers from the genomic DNA of Tsaiya ducks. Eight populations, a total of 566 samples, sourced from Ilan Branch, Livestock Research Institute were genotyped through novel and known markers. The population genetic variables were calculated using optional programs in order to describe and monitor the genetic variability and the genetic structures of these Tsaiya duck populations. Results: In total 24 primer pairs, including 17 novel microsatellite loci from this study and seven previously known loci, were constructed for the detection of genetic variations in duck populations. The average values for the allele number, the effective number of alleles, the observed heterozygosity, the expected heterozygosity, and the polymorphism information content were 11.29, 5.370, 0.591, 0.746, and 0.708, respectively. The results of analysis of molecular variance and principal component analysis indicated a contracting Brown Tsaiya duck cluster and a spreading White Tsaiya duck cluster. The Brown Tsaiya ducks and the White Tsaiya ducks with Pekin ducks were just split to six clusters and three clusters when K was set equal to 6 and 3 in the Bayesian cluster analysis. The individual phylogenetic tree revealed eight taxa, and each individual was assigned to its own population. Conclusion: According to our study, the 24 novel microsatellite markers exhibited a high capacity to analyze relationships of inter- and intra-population in those populations with a relatively limited degree of genetic diversity. We suggest that duck farms in Taiwan could use the new (novel) microsatellite set to monitor the genetic characteristics and structures of their Tsaiya duck populations at various intervals in order to ensure quality breeding and conservation strategies.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.5
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• pp.633-637
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• 2007

Genetic variation in Nilagiri sheep, the only apparel wool breed in South India was studied using 25 FAO recommended ovine-specific microsatellite markers. The number of observed alleles ranged from 3 to 8 with a mean of 5 across all loci. The size of alleles ranged from 72 to 228 bp. The frequency of alleles ranged from 0.0104 to 0.5781. In total, 125 alleles were observed at the 25 loci studied. The effective number of alleles ranged from 2.18 to 6.49. The mean number of effective alleles was 3.84 across all loci. All the 25 loci were found to be highly polymorphic. The PIC values ranged from 0.4587 to 0.8277 with a mean of 0.6485. Of 25 microsatellites studied, 17 were in Hardy-Weinberg Equilibrium proportions. The observed heterozygosity ranged from 0.4222 to 1.000 with a mean value of 0.7610 whereas the expected heterozygosity ranged from 0.5415 to 0.8459 with a mean value of 0.7213. Except six loci, the other loci revealed negative within-population inbreeding estimates (FIS) indicating excess of heterozygotes in the population of Nilagiri sheep.

• Plant Resources
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• v.1 no.2
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• pp.81-91
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• 1998

Fifty-nine Korean soybean (Glycine max L. Merr.) landrace accessions were tested for genotype fingerprinting, differentiation and association between morphological traits and SSR profile. Using 8 SSR loci, 59 varieties were divided into 55 groups, and only 4 pairs of varieties were not uniquely identified. The resolving power of SSR for soybean genotyping was much higher than that of the morphological traits that were studied. Identification efficiency also differed among SSR loci. Those loci with higher numbers of alleles distinguished varieties more effectively. Genetic differentiation values of the soybean landraces varied from 0.57 to 0.82 with a mean of 0.68. The number of alleles detected by the 8 loci ranged from 3 to 8. and the effective number of alleles ranged from 2.3 to 5.1. In a study of the association of SSR alleles with morphological traits, some alleles seemed to be related with some specific morphological traits. Comparison of two kinds of dendrograms which were derived from SSR markers and quantitative traits indicated that the dendrograms were not consistent. Considering the correlation between single SSR locus and qualitative traits governed by major genes, the data suggest that alleles of microsatellite loci be more closely related to some traits determined by major genes than those determined by minor genes.

• Communications for Statistical Applications and Methods
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• v.13 no.3
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• pp.525-535
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• 2006

We describe tests for detecting and locating quantitative traits loci (QTL) for traits in Hanwoo. Lod scores and a permutation test have been described. From results of a permutation test to detect QTL, we select major DNA markers of ILSTS098 microsatellite locus in Hanwoo chromosome 2 for further analysis. K-means clustering analysis applied to four traits and eight DNA markers in ILSTS098 resulted in three cluster groups. We conclude that the major DNA markers of BMS1167 microsatellite locus in Hanwoo chromosome 2 are markers 105bp, 113bp and 115bp. Finally, bootstrap testing method has been adapted to calculate confidence intervals and for finding major DNA Markers.

• Journal of Veterinary Clinics
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• v.15 no.2
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• pp.274-278
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• 1998

The biological father of two Golden Retriever puppies was determined between two proposed stud dogs by using microsatellite DNA analysis. DNA was obtained from all the relevant dogs by buccal swabbing and three loci of tetranucleotide repeat microsatellite were PCR-amplifiedl and analyzed by polyacrylamide gel electrophoresis and silver staining. One of the two proposed stud dogs was assigned as the biological father of the puppies by the genotyping. The result demonstrated that the microsatellite DNA analysis is a simple, efficient method of paternity test in dogs.

• Animal Bioscience
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• v.35 no.9
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• pp.1314-1326
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• 2022

Objective: Alongside the rise of animal-protection awareness in Taiwan, the public has been paying more attention to dog genetic deficiencies due to inbreeding in the pet market. The goal of this study was to isolate novel microsatellite markers for monitoring the genetic structure of domestic dog populations in Taiwan. Methods: A total of 113 DNA samples from three dog breeds-beagles (BEs), bichons (BIs), and schnauzers (SCs)-were used in subsequent polymorphic tests applying the 14 novel microsatellite markers that were isolated in this study. Results: The results showed that the high level of genetic diversity observed in these novel microsatellite markers provided strong discriminatory power. The estimated probability of identity (P_(ID)) and the probability of identity among sibs (P_(ID)sib) for the 14 novel microsatellite markers were 1.7×10^-12 and 1.6×10^-5, respectively. Furthermore, the power of exclusion for the 14 novel microsatellite markers was 99.98%. The neighbor-joining trees constructed among the three breeds indicated that the 14 sets of novel microsatellite markers were sufficient to correctly cluster the BEs, BIs, and SCs. The principal coordinate analysis plot showed that the dogs could be accurately separated by these 14 loci based on different breeds; moreover, the Beagles from different sources were also distinguished. The first, the second, and the third principal coordinates could be used to explain 44.15%, 26.35%, and 19.97% of the genetic variation. Conclusion: The results of this study could enable powerful monitoring of the genetic structure of domestic dog populations in Taiwan.

• 한국수산학회:학술대회논문집
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• 2005.05a
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• pp.219-220
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• 2005

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.11
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• pp.1524-1528
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• 2005

Molecular genetic markers were used to detect chromosomal regions which contain economically important traits such as growth, carcass, and meat quality traits in pigs. A three generation resource population was constructed from a cross between Korean native boars and Landrace sows. A total of 240 F2 animals from intercross of F1 was produced. Phenotypic data on 17 traits, birth weight, body weights at 3, 5, 12, and 30 weeks of age, teat number, carcass weight, backfat thickness, body fat, backbone number, muscle pH, meat color, drip loss, cooking loss, water holding capacity, shear force, and intramuscular fat content were collected for F2 animals. Animals including grandparents (F0), parents (F1), and offspring (F2) were genotyped for 80 microsatellite markers covering from chromosome 1 to 10. Least squares regression interval mapping was used for quantitative trait loci (QTL) identification. Significance thresholds were determined by permutation tests. A total of 10 QTL were detected at 5% chromosome-wide significance levels for growth traits on SSCs 2, 4, 5, 6, and 8.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.47 no.1
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• pp.52-58
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• 2014

Morphological and genetic variation of two populations of Platichthys stellatus were investigated based on 30 individuals each, collected from Uljin (seedling release area) and Pohang (control) in Korea. Morphological analyses demonstrated that the two populations of P. stellatus were well distinguishable in body color of the blind side and fin shape. Mitochondrial DNA control region analysis indicated no significant differences between the two populations ($F_{ST}=-0.00849$, P>0.05). We also analyzed microsatellite DNA loci of the two populations using six markers. Observed heterozygosity ($H_O$) and expected heterozygosity ($H_E$) were 0.550 and 0.592, respectively, in P. stellatus from Uljin, but 0.700 and 0.737 in P. stellatus from Pohang. An index of differentiation in genetic structure revealed significant differences between the two populations ($F_{ST}=0.0208$, P<0.05). Our results suggest that the Uljin population may be comprised of released P. stellatus, whereas the Pohang population may be wild P. stellatus, highlighting the necessity of continuous monitoring of the two populations.