• Title, Summary, Keyword: Genetic Diversity Loss

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Comparative genetic diversity of wild and released populations of Pacific abalone Haliotis discus discus in Jeju, Korea, based on cross-species microsatellite markers including two novel loci

  • An, Hye-Suck;Hong, Seong-Wan;Kim, En-Mi;Lee, Jeong-Ho;Noh, Jae-Koo;Kim, Hyun-Chul;Park, Chul-Ji;Min, Byung-Hwa;Myeong, Jeong-In
    • Animal cells and systems
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    • v.14 no.4
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    • pp.305-313
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    • 2010
  • Pacific abalone Haliotis discus discus is an important fisheries resource in Jeju, Korea. For basic information about its current genetic status in relation to stock enhancement, the level and distribution of genetic variation between wild and released stocks of Pacific abalone in Jeju were examined at nine cross-species microsatellite markers including the use of two novel primers. High levels of polymorphism were observed between the two populations. A total of 146 different alleles were found at all loci, with some alleles being unique. The allelic variability ranged from five to 27 in the wild population and from four to 16 in the released sample. The average observed and expected heterozygosities were estimated to be 0.74 and 0.84 in the wild sample and 0.70 and 0.78 in the released sample, respectively. Although a considerable loss of rare alleles was observed in the released sample, no statistically significant reductions were found in heterozygosity or allelic diversity in the released sample compared to the wild population. Low but significant genetic differentiation was found between the wild and released populations. These results suggest that the intensive breeding practices for stock enhancement may have resulted in a further decrease in genetic diversity, and that the cross-species microsatellite markers used in this study represent a potentially efficient means for further genetic studies, providing beneficial information for the protection and management of H. discus discus.

No Genetic Differentiation of Elaphe schrenckii Subspecies in Korea Based on 9 Microsatellite Loci

  • An, Jung-Hwa;Park, Dae-Sik;Lee, Jung-Hyun;Kim, Kyung-Seok;Lee, Hang;Min, Mi-Sook
    • Animal Systematics, Evolution and Diversity
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    • v.26 no.1
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    • pp.15-19
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    • 2010
  • The Russian ratsnake, Elaphe schrenckii, is found in Russia, China, and Korea, and is considered to be an endangered species by the Ministry of Environment in South Korea. Due to habitat loss and use in oriental medicine, their population has been severely decimated. In South Korea, two subspecies of E. schrenckii has been defined according to body color: E. s. schrenckii (blackish) and E. s. anomala (yellow-brownish). Molecular genetic studies on Elaphe schrenckii are very scarce and the taxonomy of Elaphe schrenckii subspecies is uncertain. From the present study, we attempted to identify the genetic differences of these two subspecies using species-specific microsatellites developed from the genomic library of E. schrenckii. Nine polymorphic loci were tested on 19 individuals from E. s. schrenckii (n=10) and E. s. anomala (n=9) in South Korea. The mean number of alleles was 3.78 in E. s. schrenckii and 4.11 in E. s. anomala. The average expected heterozygosity was 0.542 and 0.511 in E. s. schrenckii and E. s. anomala, respectively. We found a lack of genetic structure between two subspecies ($F_{ST}=0.016$) and no genetic discrimination between two subspecies was found. Based on the present findings by microsatellites, two subspecies can be considered as one species, E. schrenckii. However, further investigations on taxonomical status using mitochondrial and nuclear DNA sequences need to be performed and morphological & ecological data should be revised. The genetic markers should benefit future studies of the endangered species of other Elaphe species for the study of genetic diversity and potential conservation management.

Investigation of Genetic Diversity between Wild-caught and Hatchery-reared Rock Bream (Oplegnathus fasciatus) Using Microsatellite DNA Analysis

  • Kim, Mi-Jung;An, Hye-Suck;Hong, Seong-Wan;Park, Jung-Youn
    • Fisheries and aquatic sciences
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    • v.11 no.2
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    • pp.82-87
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    • 2008
  • Marine fisheries are important natural resources and must be maintained, especially fish species that are important sources of food. Despite the increase in stocking programs to maintain fisheries with artificially raised fish, the genetic impact stocking has on the wild fry population has not been addressed. Genetic variation in rock bream, Oplegnathus fasciatus, within and between wild-caught parents and the $F_1$ generation produced by them in 1 day was assayed using nine highly variable micro satellite markers. The nine micro satellite loci used in this study displayed diverse polymorphisms, and in total, 98 different alleles were observed over all loci. Differences in genetic variability of the $F_1$ offspring compared to their wild-caught parents (brood stock) were observed in terms of allele frequency, gene diversity, and heterozygosity. Although the $F_1$ generation of rock bream was missing 16% of the micro satellite alleles, no significant reduction was found in mean heterozygosity of the $F_1$ population compared to the brood stock. Eight of nine loci showed significant Hardy-Weinberg equilibrium (HWE) deviations in the $F_1$ population, while the brood stock deviated from HWE at three micro satellite loci (KOF85, KOF360 and KOF374). These deviations showed mostly a deficit of heterozygotes. Our results provide evidence for genetic differences in the $F_1$ hatchery offspring compared to their wild-caught parents and reinforce the need for a series of consecutive egg collections to avoid the loss of genetic variability. This also further underscores the importance of monitoring genetic variability of hatchery populations for the conservation of natural rock bream resources.

Genetic diversity and phylogenetic relationship analyzed by microsatellite markers in eight Indonesian local duck populations

  • Hariyono, Dwi Nur Happy;Maharani, Dyah;Cho, Sunghyun;Manjula, Prabuddha;Seo, Dongwon;Choi, Nuri;Sidadolog, Jafendi Hasoloan Purba;Lee, Jun-Heon
    • Asian-Australasian Journal of Animal Sciences
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    • v.32 no.1
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    • pp.31-37
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    • 2019
  • Objective: At least eight local duck breeds have been recognized and documented as national germplasm of Indonesia so far. It is necessary to genetically characterize the local duck breeds for aiding conservation and future improvement strategies. Thus, this study was carried out to assess genetic diversity and phylogenetic relationship of eight local duck populations of Indonesia using microsatellite markers. Methods: In total, 240 individuals (30 individuals each population) from Alabio (AL), Bayang (BY), Magelang (MG), Mojosari (MJ), Pegagan (PG), Pitalah (PT), Rambon (RM), and Turi (TR) duck populations were genotyped using 22 microsatellite markers. Results: The results showed a moderate level of genetic diversity among populations, with a total of 153 alleles detected over all loci and populations, ranging from 3 to 22 alleles per locus. Observed (Ho) and expected heterozygosity (He), as well as polymorphism information content over all loci and populations were 0.440, 0.566, and 0.513, respectively. Heterozygote deficiency in the overall populations ($F_{IT}=0.237$), was partly due to the heterozygote deficiency within populations ($F_{IS}=0.114$) and moderate level of genetic differentiation among populations ($F_{ST}=0.137$). The most diverse population was MG (He = 0.545) and the least diverse population was AL (He = 0.368). The majority of populations were relatively in heterozygote deficiency (except AL), due to inbreeding. The genetic distances, phylogenetic trees, and principal coordinates analysis concluded that the populations can be grouped into two major clusters, resulting AL, MG, and MJ in one cluster separated from the remaining populations. Conclusion: The present study revealed a considerable genetic diversity of studied populations and thus, proper management strategies should be applied to preserve genetic diversity and prevent loss of alleles.

Genetic Variation in Geographically Peripheral Populations of Bupleurum euphorbioides (Apiaceae) with Comparison to a Widespread Congener, B. longiradiatum

  • Kim, Hui;Chang, Chin-Sung
    • Animal cells and systems
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    • v.9 no.1
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    • pp.27-35
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    • 2005
  • Bupleurum euphorbioides is isolated and restricted to high mountains in Korea northeastern China. Its conservation depends on whether it is threatened by inbreeding or a loss of genetic diversity. We compared the genetic variability in B. euphorbioides with B. longiradiatum, a widespread congener, to understand how they differ in their population genetic structure. Although B. euphorbioides showed a little lower genetic variability than B. longiradiatum, $F_{IS}$ statistics for most loci were strongly positive in both B. euphorbioides (0.445) and B. longiradiatum (0.553). In addition, B. euphorbioides showed higher mean $F_{ST}$ value than B. longiradiatum (0.297 vs 0.194). It might be due to the polycarpic nature of B. longiradiatum, which holds higher genetic potentials effectively in homogeneous environment than the monocarpic B. euphorbioides. The results suggested that B. euphorbioides is a genetically viable species, and that they are threatened primarily by environmental factor.

Smallest-Small-World Cellular Genetic Algorithms (최소좁은세상 셀룰러 유전알고리즘)

  • Kang, Tae-Won
    • Journal of KIISE:Software and Applications
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    • v.34 no.11
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    • pp.971-983
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    • 2007
  • Cellular Genetic Algorithms(CGAs) are a subclass of Genetic Algorithms(GAs) in which each individuals are placed in a given geographical distribution. In general, CGAs# population space is a regular network that has relatively long characteristic path length and high clustering coefficient in the view of the Networks Theory. Long average path length makes the genetic interaction of remote nodes slow. If we have the population#s path length shorter with keeping the high clustering coefficient value, CGAs# population space will converge faster without loss of diversity. In this paper, we propose Smallest-Small-World Cellular Genetic Algorithms(SSWCGAs). In SSWCGAs, each individual lives in a population space that is highly clustered but having shorter characteristic path length, so that the SSWCGAs promote exploration of the search space with no loss of exploitation tendency that comes from being clustered. Some experiments along with four real variable functions and two GA-hard problems show that the SSWCGAs are more effective than SGAs and CGAs.

Determination of Genetic Diversity among Korean Hanwoo Cattle Based on Physical Characteristics

  • Choi, T.J.;Lee, S.S.;Yoon, D.H.;Kang, H.S.;Kim, C.D.;Hwang, I.H.;Kim, C.Y.;Jin, X.;Yang, C.G.;Seo, K.S.
    • Asian-Australasian Journal of Animal Sciences
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    • v.25 no.9
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    • pp.1205-1215
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    • 2012
  • This study was conducted to establish genetic criteria for phenotypic characteristics of Hanwoo cattle based on allele frequencies and genetic variance analysis using microsatellite markers. Analysis of the genetic diversity among 399 Hanwoo cattle classified according to nose pigmentation and coat color was carried out using 22 microsatellite markers. The results revealed that the INRA035 locus was associated with the highest $F_{is}$ (0.536). Given that the $F_{is}$ value for the Hanwoo INRA035 population ranged from 0.533 (white) to 1.000 (white spotted), this finding was consistent with the loci being fixed in Hanwoo cattle. Expected heterozygosities of the Hanwoo groups classified by coat colors and degree of nose pigmentation ranged from $0.689{\pm}0.023$ (Holstein) to $0.743{\pm}0.021$ (nose pigmentation level of d). Normal Hanwoo and animals with a mixed white coat showed the closest relationship because the lowest $D_A$ value was observed between these groups. However, a pair-wise differentiation test of $F_{st}$ showed no significant difference among the Hanwoo groups classified by coat color and degree of nose pigmentation (p<0.01). Moreover, results of the neighbor-joining tree based on a $D_A$ genetic distance matrix within 399 Hanwoo individuals and principal component analyses confirmed that different groups of cattle with mixed coat color and nose pigmentation formed other specific groups representing Hanwoo genetic and phenotypic characteristics. The results of this study support a relaxation of policies regulating bull selection or animal registration in an effort to minimize financial loss, and could provide basic information that can be used for establishing criteria to classify Hanwoo phenotypes.

The Causes of Deforestation and Loss of Genetic Resources in Bangladesh

  • Islam, Mohammad Saiful;Islam, Mohammad Jahidul;Ahmed, Sheikh Ali;Chun, Su-Kyoung;Chong, Song-Ho;Kim, Jong-In
    • Journal of the Korea Furniture Society
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    • v.18 no.4
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    • pp.317-323
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    • 2007
  • Almost all the people, particularly the rural people are directly dependent on the continued productivity of natural resources, like water, soils, forests and fisheries. But the overuse by the extremely high population pressures has degraded the natural resources into severe widespread deforestation. The degradation of natural resources, particularly the plant resources has been a great concern for socio-economic and sustainable development of the country. The Forests in Bangladesh have been depleted and degraded in volume, area, and quantity, thus requiring urgent forest protection by identifying the causes of forest loss. There are so many causes of deforestation and loss of genetic resources such as; the timber industry, which, legal or not, are cutting too many trees; indigenous forest dwellers, having their own types of problems; migrants, who, because of problems in their places of origin, have decided to move to the forests and the government through its Forest Department which is not able or willing to implement suitable policies to regulate the cutting trees and to prevent illegal cutting. Because it is a time consuming task to mitigate the first and second sets of factors, we recommend involving forest dwellers in forestry practices as much as possible and taking necessary steps to alleviate the third and fourth sets and thereby reduce the rate of forest depletion. Accordingly, a number of strategies that should be adopted to halt the loss of remaining forest cover are discussed.

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Sequence Diversity of Mitochondrial Cytochrome b Gene in Grey Goral Naemorhedus caudatus(Artiodactyla, Bovidae) from Korea (한국의 산양(우제목, 소과)의 미토콘드리아 Cytochrome b 염기서열 다양성)

  • Koh, Hung-Sun;Yang, Byong-Guk;Lee, Bae-Kun;Lee, Jong-Hyong
    • Animal Systematics, Evolution and Diversity
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    • v.18 no.1
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    • pp.13-21
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    • 2002
  • To add genetic information to the conservation efforts on grey coral (Naemorhedus caudatus) in Korea, we investigated the pattern of mitochondrial cytochrome b gene sequence (606 bp) of six specimens from two localities in Korea. The corresponding sequences of N. caudatus in China obtained from GenBank were also used. The nucleotide Tamura-Nei distances between each of four haplotypes of N. caudatus in Korea and the haplotype of N. caudatus in China varied from 0.0650 to 0.0803: N. caudatus revealed high level of sequence diversity in Bovidae. In N. caudatus in Korea, the distances among three haplotypes at Yanggu were 0.0151 to 0.0185, and it suggests that the genetic diversity of Yanggu population was decreased in low level. Moreover, the distances between each of three haplotypes at Yanggu and one haplotype at Samcheok were 0.0343 to 0.0489. It indicates that habitat isolation caused the continuous increase of genetic distance with geographic distance in N. caudatus, and various conservation plans for mitigating the loss of genetic diversity in Korea have to be in immediate action. To clarify the taxonomic status of N. caudatus, the sequence (276 bp) of N. goral available from GenBank were also utilized, and n goral was not distinct from N. caudatus. It suggests that they may be conspecific, but further analyses with additional specimens of two species are necessary.

Phylogeography and Population Genetic Structure of Amur Grayling Thymallus grubii in the Amur Basin

  • Ma, Bo;Lui, Tingting;Zhang, Ying;Chen, Jinping
    • Asian-Australasian Journal of Animal Sciences
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    • v.25 no.7
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    • pp.935-944
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    • 2012
  • Amur grayling, Thymallus grubii, is an important economic cold freshwater fish originally found in the Amur basin. Currently, suffering from loss of habitat and shrinking population size, T. grubii is restricted to the mountain river branches of the Amur basin. In order to assess the genetic diversity, population genetic structure and infer the evolutionary history within the species, we analysised the whole mitochondrial DNA control region (CR) of 95 individuals from 10 rivers in China, as well as 12 individuals from Ingoda/Onon and Bureya River throughout its distribution area. A total of 64 variable sites were observed and 45 haplotypes were identified excluding sites with gaps/missing data. Phylogenetic analysis was able to confidently predict two subclade topologies well supported by maximum-parsimony and Bayesian methods. However, basal branching patterns cannot be unambiguously estimated. Haplotypes from the mitochondrial clades displayed local homogeneity, implying a strong population structure within T. grubii. Analysis of molecular variance detected significant differences among the different geographical rivers, suggesting that T. grubii in each river should be managed and conserved separately.