• Asian-Australasian Journal of Animal Sciences
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• v.27 no.9
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• pp.1263-1269
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• 2014

Comprehensive information on genetic diversity and introgression is desirable for the design of rational breed improvement and conservation programs. Despite the concerns regarding the genetic introgression of Western pig breeds into the gene pool of the Korean native pig (KNP), the level of this admixture has not yet been quantified. In the present study, we genotyped 93 animals, representing four Western pig breeds and KNP, using the porcine SNP 60K BeadChip to assess their genetic diversity and to estimate the level of admixture among the breeds. Expected heterozygosity was the lowest in Berkshire (0.31) and highest in Landrace (0.42). Population differentiation ($F_{ST}$) estimates were significantly different (p<0.000), accounting for 27% of the variability among the breeds. The evidence of inbreeding observed in KNP (0.029) and Yorkshire (0.031) may result in deficient heterozygosity. Principal components one (PC1) and two (PC2) explained approximately 35.06% and 25.20% of the variation, respectively, and placed KNP somewhat proximal to the Western pig breeds (Berkshire and Landrace). When K = 2, KNP shared a substantial proportion of ancestry with Western breeds. Similarly, when K = 3, over 86% of the KNP individuals were in the same cluster with Berkshire and Landrace. The linkage disquilbrium (LD) values at $r^2_{0.3}$, the physical distance at which LD decays below a threshold of 0.3, ranged from 72.40 kb in Landrace to 85.86 kb in Yorkshire. Based on our structure analysis, a substantial level of admixture between Western and Korean native pig breeds was observed.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.9
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• pp.1407-1414
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• 2018

Objective: The aim of this study was to estimate (co) variance components and genetic parameters for categorical carcass traits using Bayesian inference via mixed linear and threshold animal models in Anglonubian goats. Methods: Data were obtained from Anglonubian goats reared in the Brazilian Mid-North region. The traits in study were body condition score, marbling in the rib eye, ribeye area, fat thickness of the sternum, hip height, leg perimeter, and body weight. The numerator relationship matrix contained information from 793 animals. The single- and two-trait analyses were performed to estimate (co) variance components and genetic parameters via linear and threshold animal models. For estimation of genetic parameters, chains with 2 and 4 million cycles were tested. An 1,000,000-cycle initial burn-in was considered with values taken every 250 cycles, in a total of 4,000 samples. Convergence was monitored by Geweke criteria and Monte Carlo error chain. Results: Threshold model best fits categorical data since it is more efficient to detect genetic variability. In two-trait analysis the contribution of the increase in information and the correlations between traits contributed to increase the estimated values for (co) variance components and heritability, in comparison to single-trait analysis. Heritability estimates for the study traits were from low to moderate magnitude. Conclusion: Direct selection of the continuous distribution of traits such as thickness sternal fat and hip height allows obtaining the indirect selection for marbling of ribeye.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.6
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• pp.784-788
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• 2006

Microsatellite polymorphism and the genetic relationship were estimated using genotype information of 305 horses from 11 microsatellite loci. The breeds include the indigenous Korean breeds, Korean native horse (102) and Jeju racing horse (56) together with Japan Hokkaido horse (5), Mongolian horse (19), Thoroughbred horse (108), Quarter horse (11) and Przewalskii horse (4). Allelic frequencies, the number of alleles per locus were estimated by direct counting from observed genotype, and genetic variability was computed using the CERVUX software and DISPAN. The number of alleles per locus varied from 6 (HMS6) to 18 (ASB17) with an average value of 10.45 in horse breeds. The expected total heterozygosity ($H_T$) and coefficient of gene differentiation ($G_{ST}$) ranged 0.764-0.921 (the average value was 0.830) and 0.102-0.266 (the average value was 0.180) in horse breeds, respectively. Four populations (Przewalskii horse, Japan Hokkaido horse, Quarter horse, Thoroughbred horse) showed lower heterozygosity than the average value (the average value was 0.710). The expected heterozygosity within breed ($H_S$) and mean no. of observed alleles ranged from $0.636{\pm}0.064$ (Japan Hokkaido horse) to $0.809{\pm}0.019$ (Mongolian horse), and from 2.73 (Przewalskii horse) to 8.27 (Korean native horse), respectively. The polymorphic information content (PIC) ranged from 0.490 (Przewalskii horse) to 0.761 (Mongolian horse) with an average value of 0.637 in horse breeds. The results showed three distinct clusters with high bootstrap support: the Korean native horse cluster (Korean native horse, Mongolian horse), the European cluster (Przewalskii horse, Thoroughbred horse), and other horse cluster (Jeju racing horse, Japan Hokkaido horse, and Quarter horse). A relatively high bootstrap value was observed for the Korean native horse cluster and European cluster (87%), and the Korean native horse and Mongolian horse (82%). Microsatellite polymorphism data were shown to be useful for estimating the genetic relationship between Korean native horse and other horse breeds, and also be applied for parentage testing in those horse breeds.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.9
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• pp.1233-1237
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• 2008

The genetic variability within and among three deer species in Malaysia, namely Cervus nippon (sika), Cervus timorensis (rusa) and Cervus unicolor (sambar), were evaluated using the RAPD technique. The DNA extracted from the buffy coat of 34 sika, 38 rusa and 9 sambar were analysed using ten primers that gave bands which showed good resolution. The primers generated 164 RAPD markers in total, and these ranged in size from 150 to 900 bp. The percent of polymorphism of the bands generated per primer ranged from 66.66-93.33% for rusa, 36.84-61.14% for sambar and 52.38-100% for sika. The overall percent polymorphism observed for the 164 RAPD markers was 99.39%. The results revealed five exclusive, monomorphic markers for sambar and one exclusive, monomorphic marker for sika; none was observed for rusa. However, these cannot be declared as markers for the identification of the species without analysis of more samples, populations and species. The means of within population genetic distances, based on Dice's and Jaccard's similarity indices, were similar for the rusa (0.383 and 0.542, respectively) and sika (0.397 and 0.558, respectively) populations with the sambar population being the least variable (0.194 and 0.323, respectively). The Dice based genetic distances within the species ranged from 0.194 to 0.397 and the genetic distances among the species were 0.791-0.911. The genetic distances based on Dice's and Jaccard's similarity indices between the rusa and sambar were 0.556 and 0.713, between the rusa and sika populations were 0.552 and 0.710, and between sambar and sika were 0.622 and 0.766, respectively.

• Korean Journal of Plant Resources
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• v.24 no.6
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• pp.702-711
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• 2011

Buckwheat (Fagopyrum esculentum Moench), one of the minor crops grown in Korea belonging to the Polygonaceae family, is an annual crop widely cultivated in Asia, Europe, and America and has a character of outcrossing and self-incompatibility. The objective of this study was to analyze the genetic variability, phylogenetic relationships and population structure of buckwheat landraces of Korea using SSR markers. Ten microsatellite markers have been detected from a total of 79 alleles among the 179 buckwheat accessions were collected from Korea. The number of allele per marker locus ($N_A$) ranged from 2 (GB-FE-001, GB-FE-043 and GB-FE-055) to 31 (GB-FE-035) with an average of 7.9 alleles. GB-FE-035 was the most polymorphic with the highest PIC value 0.93. Major allele frequencies ($M_{AF}$) for the 10 polymorphic loci varied from 0.12 to 0.97 with a mean allele frequency of 0.57. The expected heterozygosity ($H_E$) values ranged from 0.05 to 0.94 with an average of 0.53. The observed heterozygosity ($H_O$) ranged from 0.06 to 0.92 with an average of 0.42. The overall polymorphic information contents (PIC) values ranged from 0.05 to 0.93 with an average of 0.48. The landrace accessions of buckwheat used in the present study were not distinctly grouped according to geographic distribution. The study concludes that the results revealed genetic differentiation was low according to the geographic region because of outcrossing and self-incompatibility. We reported that our analyses on the genetic diversity of common buckwheat cultivars of Korea were performed by using of microsatellite markers.

• Asian-Australasian Journal of Animal Sciences
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• v.13 no.4
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• pp.431-434
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• 2000

Maintaining maximum genetic variability is of critical importance with in-situ conservation of animal species in small populations. Marker-assisted mating (MAM) was suggested to achieve maximum heterozygosity in offspring populations. The aims of this research was to investigate and decide the effectiveness and promising types of MAM to achieve this goal. Analysis of variance with simulation data revealed that the heterozygosity in offspring populations was significantly determined by sire heterozygosity from mating of non-inbred parent animals, and significantly by sire heterozygosity and percent parental difference in offspring reproduced by inbred parents. Seven types of marker-assisted mating schemes were examined, in which offspring exhibited heterozygosity that was -0.01 to 7.37% below or above that from random mating of non-inbred parent animals, and 0.00 to 16.39% above that from random mating of inbred parent animals. The great increase in offspring heterozygosity was observed with mating by tandem maximizing sire heterozygosity, percent parental difference, and dam heterozygosity. Random mating resulted in fluctuation of offspring heterozygosity. These results suggested that MAM was a promising method for maintaining maximum offspring variability in in-situ conservation of animal species in small populations.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.2
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• pp.173-180
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• 2011

Osteocalcin (OC), a marker of bone turnover, displays patterns in relation to physiological and genetic factors. Here, we present an association study in a population of Chinese Holstein cattle (n = 24) with OC serum concentration as a phenotypic trait. We hypothesised that OC status is associated with phylogeny, vitamin D serum level and single nucleotide polymorphisms (SNPs). Mitochondrial DNA (mtDNA) was used as an unlinked marker to examine phylogeny and linkage to measured phenotypic traits of vitamin D and OC status. Following an association study with OC serum variability as the trait, genotyping of SNPs (n = 27) in OC-related genes was performed. Candidate SNPs were chosen in genes with an emphasis on the vitamin D and vitamin K pathways. Multivariant factor analysis revealed a correlation between vitamin D serum concentration and a SNP in the gene GC (rs43338565), which encodes a vitamin D-binding protein, as well as between a SNP in NFATc1 (rs42038422) and OC concentration. However, univariate analysis revealed that population structure, vitamin D serum levels and SNPs were not significant determinants of OC status in the studied group.

• 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.

• Korean Journal of Medicinal Crop Science
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• v.4 no.3
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• pp.224-230
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• 1996

Randomly amplified polymorphic DNA(RAPD) analysis was applied to detect the molecular polymorphisms in Gentiana scabra var. buergeri. A high level of molecular variability was found among wild plants and cultivars. In genetic analysis, eight of twenty primers were selected and 54 amplification products ranged 2. 2 to 0.2 kb were compared. Twenty - nine amplified products showed polymorphic, while five were monomorphic. Twenty of line specific bands were found. In genetic similarity and cluster analysis using PCR products, three wild plants collected from Naejangsan, Daedunsan and Keojedo and one cultivar Seochunjaerae were grouped into one cluster, while cultivar Jinbujaerae and Japanese line separated into another clusters, respectively. The identification of DNA polymorphisms by the RAPD technique will facilitate the selection of the lines from different origin.

• Journal of Life Science
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• v.20 no.9
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• pp.1287-1293
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• 2010

The spatial distribution of alleles and geographical distances of a Carex humilis population on Mt. Giri in Korea were studied. A total of 102 DNA fragments (bands) were found among 107 plants. Among these 102 bands, 48 (47.1%) bands were polymorphic. In a simple variability of subpopulations by the percentage of polymorphic bands, distances I and V exhibited the lowest variation (16.7%). Distance VIII showed the highest variation (22.6%). The total genetic diversity (H) was 0.076 across species. Class VIII had the highest H (0.093), while class I had the lowest (0.063). Genetic similarity of individuals was found among subpopulations at up to a scale of 60 m distance, and this was partly due to a combination of alleles. Within the Mt. Giri population, a strong spatial structure was observed for RAPD markers, indicating a very low amount of migration among subpopulations and that the distribution of individual genotypes of a given population was clumped. The present study demonstrated that analysis of RAPD markers could be successfully used to study the spatial and genetic structures of C. humilis.