• Asian-Australasian Journal of Animal Sciences
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• v.19 no.5
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• pp.622-626
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• 2006

Molecular characterization of Hallikar, the native cattle breed of Karnataka, was undertaken using 19 cattle specific, highly polymorphic microsatellite markers recommended by FAO. The genomic DNA was subjected to PCR amplification and alleles were resolved through six per cent denaturing PAGE with a 10 bp DNA ladder followed by silver staining. Genotyping of animals was done based on allele size. The number of alleles ranged from three to nine with allele sizes ranging from 102 bp to 294 bp. These alleles were distributed in the frequency range between 0.0306 and 0.8673 in the population. The mean observed number of alleles was $6.368{\pm}1.4225$. The mean observed and expected heterozygosities were $0.7515{\pm}0.1734$ and $0.7850{\pm}0.1381$, respectively. The high heterozygosity observed implies presence of higher genetic variability within Hallikar breed. The PIC (Polymorphism Information Content) values ranged from 0.2322 (ETH152) to 0.8654 (ETH225). The percentage of polymorphic loci obtained was 100 as all the 19 microsatellite markers were found to be polymorphic. Except for ETH152, all the other loci had high PIC values, indicating that these markers are highly informative for characterization of Hallikar breed. The population was tested for Hardy-Weinberg equilibrium at 19 microsatellite loci, and at 74 per cent of the loci the population was found to be in disequilibrium.

• Biotechnology and Bioprocess Engineering:BBE
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• v.5 no.1
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• pp.23-26
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• 2000

In order to develop the specific genetic marker for Korean native cattle (Hanwoo), randomly amplified polymorphic DNA (RAPD) analysis of 6 different cattle breeds was attempted by using 38 decamer primers. In comparison of RAPD patterns, two distinctive DNA bands specific for Hanwoo were detected. One was 296 bp of DNA fragment found to be specific only for female Hanwoo when primer GTCCACACGG was employed. In individual analysis of this RAPD marker was observed only in female individuals with the possibility of $85.3\%$. The other was 521 bp of RAPD marker amplified using TCGGCGATAG and AGCCAGCGAA primers, which showed $83.0\%$ of genetic frequency in 85 male and 68 female individuals tested. Nucleotide sequencing of these genetic markers revealed that 296 bp marker has a short micro satellite-like sequence, ACCACCACAC, and a tandem repeat sequence of microsatellite GAAAAATG in the determined sequence. Two distinctive tandem repeats of microsatellite sequences, MC and GAAGA, were also appeared in 521 bp DNA marker. In BLAST search, any gene having high homology with these markers was not found.

• Journal of Life Science
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• v.16 no.3 s.76
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• pp.382-386
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• 2006

A total number of 20 cat samples including 8 parentage testing and 12 individual identification were genotyped. Genomic DNA was extracted from buccal swab, and genotyped by using 10 microsatellite markers (FCA005, FCA26, FCA224, FCA240, FCA453, FCA293, FCA075, FCA105, FCA229, and FCA651). This method consisted of single PCR procedure and showed reasonable amplification of all PCR products. Genotypes were determined by genetic analyzer. The number of alleles per locus of cats varied from 3 to 8 with a mean value of 5.5. Expected heterozygosity was ranged from 0.390 to 0.827 (mean 0.639) and the total exclusion probability of 10 microsatellite loci was 0.9441. Of the 10 markers, FCA240 marker has relatively high PIC value (>0.7). Of the 8 cats, 7 cats were qualified by compatibility according to the Mendelism. These results can give basic information for developing parentage verification and individual identification system in cat.

• Journal of Aquaculture
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• v.19 no.3
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• pp.205-209
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• 2006

Genetic change from broodstock to hatchery stock of the olive flounder Paralichthys olivaceus and effective number of breeders (Ne) were investigated by the different fertilized-egg collecting methods; E1 (eggs collected one day after spawning) and E2 (eggs collected two days after spawning) using seven microsatellite loci (Kop2, Kop22, Kop18, Kop3, Kop21, Kop9 and Kop26) for the better understanding of stock enhancement. Observed heterozygosity in three stocks ranged from 0.651 at Kop3 to 0.928 at Kop22, with offspring being slightly higher heterozygous over their parents. However, the genetic reduction of offspring was significant. The offspring allele number per locus was reduced to 23.5% for E1 and 17.6% for E2 of their maternal number. Ne to the hatchery stock was estimated to be 21.9 for E1 and 34.3 for E2. The inbreeding coefficients of populations El and E2 were 0.023 and 0.015, respectively. The present study suggests the extension of the egg collection period for a recovery of the genetic diversity in artificially produced offspring.

• Journal of Life Science
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• v.19 no.2
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• pp.174-178
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• 2009

The characteristics of the population genetic structure of the Japanese anchovy (Engraulis japonicus Temminck & Schlegel) were collected from the West, South and East Seas of Korea in August, 2006 and were compared using six microsatellite DNA loci. In the West Sea population, the range of allele number against 72 individuals was from 19 to 41, the average allele number was 28.5. In EJ9, the allele number had the highest value of 41, this was 1.4 times higher than the average number of allele. The average allele number of the South Sea population was 24.5 that was less than that of West Sea population. In EJ2, EJ9 and EJ27.1 loci, the allele number was higher than average allele number in the South Sea population. In the East Sea population, the average allele number was estimated at 25.0 that most of loci except for EJ35 were higher than average allele number. Allele frequency in the West, South and East Sea populations was below 0.24. The value of observed heterozosity for six loci was approximately 0.5 higher than that of expected heterozosity (p>0.05), but three populations similar values to these heterozosity. Although the genetic diversity was higher value of above 0.9, three populations had a similar value. Genetic differentiation and distance combined estimate of the six loci were 0.258 and 0.019 (p>0.05), respectively, but showed no significant distance between three populations. These results suggested that it is responsible for no differentiated gene pool between three populations.

• Journal of Life Science
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• v.33 no.8
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• pp.623-631
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• 2023

This study was conducted to develop microsatellite markers in Parapristipoma trilineatum using next-generation sequencing. A total of 402,244,934 reads were generated on the Illumina Hiseq X Ten System, yielding 60,738,985,034 bp of sequences. The de novo assembly resulted in 1,320,995 contigs. A total of 952,326 contigs (0.016%) including 151 microsatellite loci were derived from the 1,320,995 contigs longer than 640 bp. A total of 34 primer sets were designed from the 151 microsatellite loci. As a result, 15 microsatellite loci were chosen and used for assuming population genetic parameters in the wild and farmed populations. The mean number of effective alleles was 12, ranging from 6 to 25. The observed heterozygosity (H_O) and the expected heterozygosity (H_E) ranged between 0.530 and 0.873, with an average of 0.750, and from 0.647 to 0.895, with an average of 0.793, respectively. According to these results, the developed set of 15 microsatellite markers is expected to be useful for the analysis of genetic characteristics in the population of P. trilineatum in Korea. There are requirements now for further genetic information, fishery resource management, breeding guidelines, support with the selection of breeds and studies on the effects of release, all of which will improve species conservation, and through future research, we aim to offer genetic foundational data with that goal.

• Fisheries and Aquatic Sciences
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• v.15 no.2
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• pp.151-155
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• 2012

We used nine microsatellite DNA markers to estimate genetic variation among wild and cultured populations of the sea squirt Halocynthia roretzi. The loci were polymorphic, with 6-32 alleles, and allelic richness ranged from 6.0 to 26.1 in each population. The wild and the cultured populations had similar mean heterozygosities ($H_O$ and $H_E$), allele numbers, and allelic richness. One cultured population with softness syndrome had a lower mean in the observed heterozygosity ($H_O$ = 0.57) and higher mean inbreeding coefficient ($F_{IS}$ = 0.261) than any other populations. This suggests that the loss of genetic variation in the diseased population might be due to increased inbreeding. A neighbor-joining tree and pairwise population estimates of $F_{ST}$ showed moderate genetic differentiation between the wild and the cultured populations. Additionally, the softness syndrome population was genetically divergent from wild populations, but it was genetically close to the cultured populations.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.12
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• pp.1783-1790
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• 2007

The genetic diversity of domestic quail and two wild quail species, Japanese （Coturnix coturnix）and Common quail (Coturnix japonica), found in China was studied using microsatellite DNA markers. According to a comparison of the corresponding genetic indices in the three quail populations, such as Polymorphism Information Content (PIC), Mean Heterozygosity ($\bar{H}$) and Fixation Index, wild Common quail possessed rich genetic diversity with 4.67 alleles per site. Its values for PIC and $\bar{H}$ were the highest, 0.5732 and 0.6621, respectively. Domestic quail had the lowest values, 0.5467 and 0.5933, respectively. Wild Japanese quail had little difference in genetic diversity from domestic quail. In addition, from analyses of the fuzzy cluster based on standard genetic distance, the similarity relationship matrix coefficient between wild Japanese quail and domestic quail was 0.937, and that between wild Common quail and domestic quail was 0.783. All of these results showed that the wild Japanese quail were closer to the domestic quail for phylogenetic relationship than wild Common quail. These results at the molecular level provide useful data about quail's genetic background and further supported the hypothesis that the domestic quail originated from the wild Japanese quail.

• 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.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.50 no.6
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• pp.806-811
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• 2017

A multiplex PCR system comprising 14 microsatellite markers was developed for genotyping analysis of the sea cucumber Stichopus japonicus. A total of 286 samples were used to evaluate genetic polymorphisms and forensic parameters of the microsatellite loci. In a single PCR reaction, all 14 loci were uniformly amplified and a total of 269 alleles were identified. The AJ19024 locus had the largest number of alleles (46), and its discriminatory power and exclusion power were 0.99 and 0.76, respectively. The fewest alleles (8) were present at the Psj2575 locus, which provided the lowest discriminatory power (0.81) and exclusion power (0.20). The mean number of alleles, mean heterozygosity, mean discrimination power and mean exclusion power per locus were 19.21, 0.70, 0.93, and 0.46, respectively. The combined matching probability for the 14 loci was $9.64{\times}10^{-19}$, and the combined power of exclusion was 0.999995. Thus, the forensic parameters evaluated in the present study demonstrated the utility of our multiplex PCR system for biological tracing methods, such as individual identification and paternity testing, in the sea cucumber.