• Asian-Australasian Journal of Animal Sciences
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• v.20 no.11
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• pp.1631-1635
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• 2007

Japanese Brown cattle, one of the four domestic beef breeds in Japan, are suffering from numerical reduction due to economic pressure from profitable breeds. In this study, all the reproductive cows in the Kouchi sub-breed of the Japanese Brown cattle that were alive in July 2005 were investigated by pedigree analysis to clarify genetic structure and composition of genetic variability. In addition, genetically important individuals for the maintenance of genetic variability of the sub-breed were also identified through the core set method. The number of cows analyzed was 1,349. Their pedigrees were traced back to ancestors born around 1940, and pedigree records of 13,157 animals were used for the analysis. Principal component analysis was performed on the relationship matrix of the cows, and their factor loadings were plotted on a three-dimensional diagram. According to their spatial positions in the diagram, all the cows were subdivided into five genetically distinctive subpopulations of 131 to 437 animals. Genetic diversity of the whole sub-breed, which is estimated to be 0.901, was decomposed into 0.856 and 0.045 of within-subpopulation and between-subpopulation components. Recalculation of genetic diversity after removal of one or several subpopulations from the five subpopulations suggested that three of them were genetically important for the maintenance of genetic variability of the sub-breed. Applying the core set method to all the cows, maximum attainable genetic diversity was estimated to be 0.949, and optimal genetic contributions assigned to each cow supported the previous results indicating relative importance of the three subpopulations as useful genetic materials.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.106-106
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• 2017

The soybean [Glycine max (L.) Merr.] is one of the most important crop resources worldwide as food and forage. It is also important and valuable that to hold crop resources to have high genetic diversities. Recently, a core collection has been constructed in many plants to preserve the genetic resources of various plants. A core collection is small population to represent the genetic diversity of the total collection, and is of strategic importance as they allow the use of a small part of a germplasm collection that is representative of the total collection. Here, we developed the core collection consisting of 816 accessions by using approximately 180,000 (180K) single nucleotide polymorphisms (SNPs) developed in previous study. In addition, we performed genetic diversity and population structure analysis to construct the core collection from entire 4,392 collections. there were excluded sample call rates less than 93% and duplicated samples more than 99.9% according to genotype analysis using 180K SNPs from entire collections. Furthermore, we were also excluded natural hybrid resources which Glycine max and Glycine soja are mixed in half through population structure analysis. As a result, we are constructed the core collection of genetic diversity that reflects 99% of the entire collections, including 430 cultivated soybeans (Glycine max) and 386 wild soybeans (Glycine soja). The core collection developed in this study should be to provide useful materials for both soybean breeding programs and genome-wide association studies.

• Korean Journal of Ichthyology
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• v.21 no.sup1
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• pp.52-62
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• 2009

Environmental differences of each sea around the Korean Peninsula in terms of factors including topography and complexity of sea current may influence species and genetic diversity of marine fishes. Fish are naturally abundant in the frontal area where various currents or water masses meet. However, this food resource is prone to human overexploitation, threatening the marine ecosystem. New fisheries resources management strategies are needed. Such strategies require information about population structure obtained through morphological and genetic methods.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.41 no.6
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• pp.466-470
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• 2008

Microsatellite DNA markers were used to investigate the genetic diversity and population structure of Pacific abalone Haliotis discus hannai collected from six locations (Uljin, Ulsan, Daechon, Taean, Wando, and Yosu) where hatchery-produced abalone have been released intensively. There was no distinguishable difference in the observed and expected heterozygosities between the six populations and a cultured population. However, there was a difference in the number of alleles per locus: 12.8 for the cultured population and 13.8 to 15.8 for the six populations. The proportion of stocked abalone ranged from 41.1 to 92.7% for wild-caught populations with a decreasing tendency of alleles per locus for an increasing proportion of stocked abalone. A departure from Hardy-Weinberg equilibrium (HWE) assessed using the Markov chain procedure (P<0.05) was observed in the six populations and cultured population at loci Hdh145 and Hdh5l2. The pairwise Fst test (P<0.05) showed a significant difference between the Uljin and Ulsan populations and four remaining populations (Wando, Daechon, Yosu, and the cultured population), among which the Wando population differed less than the other three populations (Daechon, Yosu, and the cultured population).

• Fisheries and Aquatic Sciences
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• v.15 no.1
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• pp.49-56
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• 2012

Genetic variation in the Asian shore crab Hemigrapsus sanguineus was determined from partial mitochondrial DNA (mtDNA) sequences of the cytochrome b (Cytb) gene. Samples included 143 crabs from six localities along three coastlines in South Korea. A nucleotide sequence analysis revealed 38 variable sites in a 470-bp sequence, which defined 37 haplotypes. The haplotypes were not associated geographically and had a shallow genealogy. Pairwise $F_{ST}$ tests and a two-dimensional scaling analysis revealed no significant genetic differentiation among most of the populations. The low pairwise comparison values, but significant genetic differentiation of a northeastern population from all other populations, might have been influenced by a restriction in gene flow caused by hydrographic conditions such as ocean boundaries. The high haplotype diversity, low nucleotide diversity, and time since H. sanguineus expansion in Korean coastal waters indicate rapid population growth and a recent, sudden expansion in the Late Pleistocene.

• Journal of Plant Biotechnology
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• v.33 no.2
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• pp.139-145
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• 2006

The present study is the first report of molecular variations in different accessions of Rauvolfia tetraphylla L.f, a medicinally important plant collected from seven locations of Andhra Pradesh, India. Molecular analysis was carried out using RAPD markers. Out of the 40 primers screened from OPA and OPC Kts, a total of 205 scorable polymorphic markers out of 397 total markers were generated. Polymorphism of 51.6% was found with 3 unique markers. Levels of genetic diversity within accessions i.e., the genetic distance ranged from 0.816-0.932. Cluster analysis based on Dice coefficient showed two major groups indicating that mostly in cross-pollinated plants, high levels of differentiation among accessions exists independent of geographical distance. Hence the results of the present study can be seen as a starting point for future researches on the population and evolutionary genetics of this species. Understanding such variation would also facilitate their use in various conservational management practices, rootstock breeding and hybridisation programmes.

• Journal of Korean Society of Forest Science
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• v.107 no.2
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• pp.151-157
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• 2018

This study was to analyze the genetic diversity of Quercus gilva Blume growing in Jeju Island for developing a preservation strategy. We examined the genetic diversity and structure using 6 ISSR primers and investigated 67 polymorphic ISSR amplicons in 80 trees distributed among five populations. The average of proportion of polymorphic loci were 93%, the average level of Shannon's information index was 0.237, and Nei's genetic diversity was 0.156. According to the analysis of the molecular variance (AMOVA), $F_{st}$ was 0.169 indicating there was a genetic variation among five populations. 17% of the total variation was allocated among the five populations, while the other 83% of the total variation was in individual trees in each population. The result could be due to the uneven number of trees among the five populations. Based on these results, the preservation strategy could be developed, for examples, considering for designation as "forest genetic resources conservation area" about the habitat, monitoring continuously, fostering the growth of seedling, ex situ preservation of genetic resources, and comparing the differences of environmental and genetic characteristic with population in ex situ.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.11
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• pp.1691-1699
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• 2018

Objective: In Korea, there are three main cattle breeds, which are distinguished by coat color: Brown Hanwoo (BH), Brindle Hanwoo (BRH), and Jeju Black (JB). In this study, we sought to compare the genetic diversity and divergence among there Korean cattle breeds using a BovineHD chip genotyping array. Methods: Sample data were collected from 168 cattle in three populations of BH (48 cattle), BRH (96 cattle), and JB (24 cattle). The single-nucleotide polymorphism (SNP) genotyping was performed using the Illumina BovineHD SNP 777K Bead chip. Results: Heterozygosity, used as a measure of within-breed genetic diversity, was higher in BH (0.293) and BRH (0.296) than in JB (0.266). Linkage disequilibrium decay was more rapid in BH and BRH than in JB, reaching an average $r^2$ value of 0.2 before 26 kb in BH and BRH, whereas the corresponding value was reached before 32 kb in JB. Intra-population, interpopulation, and Fst analyses were used to identify candidate signatures of positive selection in the genome of a domestic Korean cattle population and 48, 11, and 11 loci were detected in the genomic region of the BRH breed, respectively. A Neighbor-Joining phylogenetic tree showed two main groups: a group comprising BH and BRH on one side and a group containing JB on the other. The runs of homozygosity analysis between Korean breeds indicated that the BRH and JB breeds have high inbreeding within breeds compared with BH. An analysis of differentiation based on a high-density SNP chip showed differences between Korean cattle breeds and the closeness of breeds corresponding to the geographic regions where they are evolving. Conclusion: Our results indicate that although the Korean cattle breeds have common features, they also show reliable breed diversity.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.4
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• pp.453-457
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• 2005

The genetic variations in three major river populations viz. the Halda, the Jamuna and the Padma of the Indian major carp, Catla catla were analyzed by Random Amplified Polymorphic DNA (RAPD) markers. Four decamer primers were used for amplifying DNA of 10 individuals from each population. The proportion of polymorphic loci and the gene diversity estimates were 59.4 and 0.20 for the Halda, 37.5 and 0.14 for the Jamuna and 46.9 and 0.16 for the Padma populations respectively indicating the existence of a relatively high level of genetic variation in the Halda river population. The inter-population similarity indices, gene flow and genetic distance values indicated that the Jamuna-Padma population pair of catla was genetically closer than the Halda-Jamuna and the Halda-Padma population pairs in compliance with the geographical distances among them. The coefficient of gene differentiation ($G_{ST}$=0.13) reflects some degree of genetic differentiation among three populations of catla studied. The data suggest that the RAPD technique could be used to discriminate different river populations of catla.

• Proceedings of the Zoological Society Korea Conference
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• 1994.10a
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• pp.239.1-239
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• 1994

No Abstract, See Full Text