• Proceedings of the National Institute of Ecology of the Republic of Korea
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• v.2 no.2
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• pp.120-128
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• 2021

The objective of this study was to analyze the genotype of black-spotted pond frog (Pelophylax nigromaculatus) using seven microsatellite loci to quantify its genetic diversity and population structure throughout the spatial scale of basins of Han, Geum, Yeongsan, and Nakdong Rivers in South Korea. Genetic diversities in these four areas were compared using diversity index and inbreeding coefficient obtained from the number and frequency of alleles as well as heterozygosity. Additionally, the population structure was confirmed with population differentiation, Nei's genetic distance, multivariate analysis, and Bayesian clustering analysis. Interestingly, a negative genetic diversity pattern was observed in the Han River basin, indicating possible recent habitat disturbances or population declines. In contrast, a positive genetic diversity pattern was found for the population in the Nakdong River basin that had remained the most stable. Results of population structure suggested that populations of black-spotted pond frogs distributed in these four river basins were genetically independent. In particular, the population of the Nakdong River basin had the greatest genetic distance, indicating that it might have originated from an independent population. These results support the use of genetics in addition to designations strictly based on geographic stream areas to define the spatial scale of populations for management and conservation practices.

• Korean Journal of Poultry Science
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• v.43 no.2
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• pp.63-76
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• 2016

The genetic diversity of Korean native chicken is important for conservation of native chicken breeds and developing economically valuable traits in Korea. In this review, various types of genetic markers using Korean native chickens were investigated, which are mtDNA variations, microsatellite markers, markers in Major Histocompatibility Complex (MHC), and single nucleotide polymorphisms (SNPs). These genetic markers are suitable for breed discrimination and diversity studies because of their high polymorphism status. Thus, the purpose of this study was to summarize the genetic markers developed in the Korean native chickens and diversity studies using these breeds. Ultimately, these markers can be used for the future studies for understanding of genetic characteristics.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.10
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• pp.1399-1405
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• 2014

The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency ($F_{IT}$) in native chicken was $0.234{\pm}0.025$. Over 30.7% of $F_{IT}$ was contributed by within-population deficiency ($F_{IS}$). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds.

• Korean Journal of Agricultural Science
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• v.48 no.4
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• pp.693-702
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• 2021

The aim of this study was to analyze the genetic diversity and distance of the Korean native black goat line. Thus far, this Korean native black goat line has not been studied intensively, especially in genetic diversity and relationship studies in comparison with other breeds. In total, eleven microsatellite (MS) markers were used to evaluate alleles from 391 Korean native black goats and foreign hybrid animals. The genetic diversity index was evaluated based on the allele distributions. Four Korean native black goat lines showed expected ranges of observed heterozygosity, expected heterozygosity, and polymorphism information content (PIC) values for use in genetic diversity research (0.509 - 0.643, 0.434 - 0.623 and 0.356 - 0.567). Lines from the Korean native black goat and foreign hybrid were clearly separated according to principal coordinates analysis (PCoA), phylogenetic tree and tended to be clustered in each Korean native black goat line. Thus, this study can be used for analyzing the genetic relationships between Korean native black goats and foreign breeds for line preservation and for fundamental information to determine breed improvement strategies.

• Journal of Species Research
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• v.7 no.4
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• pp.354-362
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• 2018

Population genetic assessment is essential for the conservation and management of endangered and rare plants. Neofinetia falcata is endangered epiphyte orchid and protected by law in Korea. In Korea, this species is only found on islands in the South Sea of Korea (including Jeju-do) and the southern coast of the Korean Peninsula. We developed nine microsatellite makers to assess the genetic diversity and population genetic structure of three populations of N. falcata. The genetic diversity at the species level was low, which can be attributed to inbreeding or fragmentation into small, isolated populations. A recent bottleneck was detected in one population, likely due to overcollection. N. falcata exhibited moderated levels of differentiation among populations, with the three populations were divided into two clusters based on genetic structure. The genetic diversity and structure of N. falcata are affected by restricted gene flow by pollen or seeds due to isolation and geographic distance. Strategies for in situ and ex situ conservation of this species are been proposed based on the results of our study.

• Journal of Animal Science and Technology
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• v.65 no.5
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• pp.912-921
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• 2023

Genetic diversity analysis is crucial for maintaining and managing genetic resources. Several studies have examined the genetic diversity of Korean domestic chicken (KDC) populations using microsatellite markers, but it is difficult to capture the characteristics of the whole genome in this manner. Hence, this study analyzed the genetic diversity of several KDC populations using high-density single nucleotide polymorphism (SNP) genotype data. We examined 935 birds from 21 KDC populations, including indigenous and adapted Korean native chicken (KNC), Hyunin and Jeju KDC, and Hanhyup commercial KDC populations. A total of 212,420 SNPs of 21 KDC populations were used for calculating genetic distances and fixation index, and for ADMIXTURE analysis. As a result of the analysis, the indigenous KNC groups were genetically closer and more fixed than the other groups. Furthermore, Hyunin and Jeju KDC were similar to the indigenous KNC. In comparison, adapted KNC and Hanhyup KDC populations derived from the same original species were genetically close to each other, but had different genetic structures from the others. In conclusion, this study suggests that continuous evaluation and management are required to prevent a loss of genetic diversity in each group. Basic genetic information is provided that can be used to improve breeds quickly by utilizing the various characteristics of native chickens.

• Development and Reproduction
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• v.24 no.4
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• pp.317-325
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• 2020

The Far Eastern catfish (Silurus asotus) is an important commercial freshwater fish in Korea. Investigation of the genetic diversity of wild and cultured domestic catfish groups is essential for the restoration of fishery resources and for increasing local revenue. However, there are relatively few genetic diversity studies on wild and cultured catfish in Korea. In the present study, we analyzed the genetic diversity and association of wild and cultured catfish using five microsatellite markers. We determined that the number of alleles per locus (N_A) ranged from 9 to 25, wherein the Jeonbuk catfish demonstrated the highest mean number of alleles per locus and the cultured catfish exhibited the lowest. The average expected heterozygosity (He) of the wild catfish samples was 0.907, and that of the cultured catfish showed was 0.875. The genetic distances (GD value) among populations of all catfish ranged from 0.138 to 0.242. Jeonnam and Jeonbuk wild catfish were located closest to each other, and the cultured group was separated from the other groups. In conclusion, the present study confirmed that the genetic diversity of wild and cultured catfish was maintained at a high level. In the case of the wild group, it is effective in maintaining diversity due to the continuous fry release by the local fish research institute. However, the genetic diversity of cultured catfish declined. Low diversity is associated with slow growth and weakened immunity, and therefore continuous monitoring is necessary.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.10
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• pp.1491-1500
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• 2019

Objective: European pigs have been imported to improve the economically important traits of Thai pigs by crossbreeding and was finally completely replaced. Currently Thai indigenous pigs are particularly kept in a small population. Therefore, indigenous pigs risk losing their genetic diversity and identity. Thus, this study was conducted to perform large-scale genetic diversity and phylogenetic analyses on the many pig breeds available in Thailand. Methods: Genetic diversity and phylogenetics analyses of 222 pigs belonging to Thai native pigs (TNP), Thai wild boars (TWB), European commercial pigs, commercial crossbred pigs, and Chinese indigenous pigs were investigated by genotyping using 26 microsatellite markers. Results: The results showed that Thai pig populations had a high genetic diversity with mean total and effective ($N_e$) number of alleles of 14.59 and 3.71, respectively, and expected heterozygosity ($H_e$) across loci (0.710). The polymorphic information content per locus ranged between 0.651 and 0.914 leading to an average value above all loci of 0.789, and private alleles were found in six populations. The higher $H_e$ compared to observed heterozygosity ($H_o$) in TNP, TWB, and the commercial pigs indicated some inbreeding within a population. The Nei's genetic distance, mean $F_{ST}$ estimates, neighbour-joining tree of populations and individual, as well as multidimensional analysis indicated close genetic relationship between Thai indigenous pigs and some Chinese pigs, and they are distinctly different from European pigs. Conclusion: Our study reveals a close genetic relationship between TNP and Chinese pigs. The genetic introgression from European breeds is found in some TNP populations, and signs of genetic erosion are shown. Private alleles found in this study should be taken into consideration for the breeding program. The genetic information from this study will be a benefit for both conservation and utilization of Thai pig genetic resources.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.1
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• pp.12-23
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• 2020

Objective: The objective of a conservation program is to maintain maximum genetic diversity and preserve the viability of a breed. However, the efficiency of a program is influenced by the ability to accurately measure and predict genetic diversity. Methods: To examine this question, we conducted a simulation in which common measures (i.e. heterozygosity) and novel measures (identity-by-descent probabilities and parental genomic components) were used to estimate genetic diversity within a conserved population using double-labeled single nucleotide polymorphism markers. Results: The results showed that the accuracy and sensitivity of identity-by-state probabilities and heterozygosity were close to identity by descent (IBD) probabilities, which reflect the true genetic diversity. Expected heterozygosity most closely aligned with IBD. All common measures suggested that practices used in the current Chinese pig conservation program result in a ~5% loss in genetic diversity every 10 generations. Parental genomic components were also analyzed to monitor real-time changes in genomic components for each male and female ancestor. The analysis showed that ~7.5% of male families and ~30% of female families were lost every 5 generations. After 50 generations of simulated conservation, 4 male families lost ~50% of their initial genomic components, and the genomic components for 24.8% of the female families were lost entirely. Conclusion: In summary, compared with the true genetic diversity value obtained using double-labeled markers, expected heterozygosity appears to be the optimal indicator. Parental genomic components analysis provides a more detailed picture of genetic diversity and can be used to guide conservation management practices.

• Parasites, Hosts and Diseases
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• v.57 no.5
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• pp.469-479
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• 2019

Plasmodium vivax is usually considered morbidity in endemic areas of Asia, Central and South America, and some part of Africa. In Thailand, previous studies indicated the genetic diversity of P. vivax in malaria-endemic regions such as the western part of Thailand bordering with Myanmar. The objective of the study is to investigate the genetic diversity of P. vivax circulating in Southern Thailand by using 3 antigenic markers and 8 microsatellite markers. Dried blood spots were collected from Chumphon, Phang Nga, Ranong and, Surat Thani provinces of Thailand. By PCR, 3 distinct sizes of $PvMSP3{\alpha}$, 2 sizes of $PvMSP3{\beta}$ and 2 sizes of PvMSP1 F2 were detected based on the length of PCR products, respectively. PCR/RFLP analyses of these antigen genes revealed high levels of genetic diversity. The genotyping of 8 microsatellite loci showed high genetic diversity as indicated by high alleles per locus and high expected heterozygosity ($H_E$). The genotyping markers also showed multiple-clones of infection. Mixed genotypes were detected in 4.8% of $PvMSP3{\alpha}$, 29.1% in $PvMSP3{\beta}$ and 55.3% of microsatellite markers. These results showed that there was high genetic diversity of P. vivax isolated from Southern Thailand, indicating that the genetic diversity of P. vivax in this region was comparable to those observed other areas of Thailand.