• Korean Journal of Poultry Science
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• v.38 no.2
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• pp.81-87
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• 2011

The study was conducted to select and optimize microsatellite (MS) markers for evaluate Korean Native Chicken (KNC) breeds in order to provide standard for the classification and breed definition of the indigenous breeds. The study also aimed to characterize and classify each KNC populations for inventory and management of avian genetic resources. A total of 462 chickens from 11 populations of chicken breeds including eight KNC breeds and three commercial chicken breeds were analyzed with 19 MS markers. KNC breeds, especially Long-Tail Chicken breeds, formed separate cluster from those commercial chicken breeds. Genetic distances between KNC populations (0.11~0.18) were relatively shorter. Genetic uniformity of KNC (except KNCR breed) (0.86~0.88) were higher than that of commercial breeds (except Cornish) (0.95~0.97). On the other hand, genetic uniformity of KNC Long Tail (KNCLT) were relatively higher (0.91~0.97). The result can be used to evaluate and manage animal genetic resources at national scale.

• Journal of Life Science
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• v.21 no.3
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• pp.385-392
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• 2011

The otter (Lutra lutra) in Korea is classified as a first grade endangered species and is managed under state control. We performed a phylogenetic analysis of the otter that inhabits the Changnyeong, Jinju, and Geoje areas in Gyeongsangnamdo, Korea using mtDNA and microsatellite (MS) markers. As a result of the analysis using the 676-bp D-loop sequence of mtDNA, six haplotypes were estimated from five single nucleotide polymorphisms. The genetic distance between the Jinju and Geoje areas was greater than distances within the areas, and the distance between Jinju and Geoje was especially clear. From the phylogenetic tree estimated using the Bayesian Markov chain Monte Carlo analysis by the MrBays program, two subgroups, one containing samples from Jinju and the other containing samples from the Changnyeong and Geoje areas were clearly identified. The result of a parsimonious median-joining network analysis also showed two clear subgroups, supporting the result of the phylogenetic analysis. On the other hand, in the consensus tree estimated using the genetic distances estimated from the genotypes of 13 MS markers, there were clear two subgroups, one containing samples from the Jinju, Geoje and Changnyeong areas and the other containing samples from only the Jinju area. The samples were not identically classified into each subgroup defined by mtDNA and MS markers. It could be inferred that the differential classification of samples by the two different marker systems was because of the different characteristics of the marker systems used, that is, the mtDNA was for detecting maternal lineage and the MS markers were for estimating autosomal genetic distances. Nonetheless, the results from the two marker systems showed that there has been a progressive genetic fixation according to the habitats of the otters. Further analyses using not only newly developed MS markers that will possess more analytical power but also the whole mtDNA are needed. Expansion of the phylogenetic analysis using otter samples collected from the major habitats in Korea should be helpful in scientifically and efficiently maintaining and preserving them.

• Reproductive and Developmental Biology
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• v.36 no.4
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• pp.243-248
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• 2012

This study was conducted to find a useful marker for gene polymorphism analysis using Microsatellite marker (MS marker) in Gyeongju Donggyeong dog. Twenty three MS marker analyzed the genetic features of DNA using 100 Gyeongju Donggyeong dogs in Gyeongju area. It was performed multiplex PCR with 3 set primer divided 9, 10 and 4 by analysis of conditions among MS markers. The results were calculated heterozygosity, polymorphic information content (PIC), allele frequency and number of allele at each locus using Microsatellite Toolkit software and Cervus 3.0 program. Total 148 alleles were genotyped to determine and average 6.43 alleles was detected. FH3381 had the highest of 15 alleles and FH2834 had the lowest of 2 alleles. Expected heterozygosity had a wide range from 0.282 to 0.876 and had average value of 0.6496. Also, Observed heterozygosity had a more wide range from 0.200 to 0.950 and had average value of 0.6404. PIC had range from 0.262 to 0.859 and average PIC was calculated 0.606. Especially, FH2998 represented the highest rate of observed heterozygosity of 0.950 and FH3381 represented the highest rate of expected heterozygosity of 0.876 and PIC of 0.859. The use of these markers was considered to be useful to study genetic traits of Gyeongju Donggyeong dog.

• Korean Journal of Poultry Science
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• v.37 no.1
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• pp.81-87
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• 2010

To estimate the genetic characteristics and cumulative power of discrimination (CPD) Korean Native Chicken. We used a total of 195 genomic DNAs from four breeds population (Korean Native Red chicken: R, Korean Native Yellow chicken: Y, Korean Native Black chicken: L, Ogal chicken: S). Frequencies of microsatellites markers were used to estimate heterozygosities and genetic distances. The lowest distance (0.05) was observed between the R and L strains and the highest distance (0.158) between the L and S strains. Korean native chicken strains (R, Y, K) have each other comparatively near genetic distance. Cumulative power of discriminate (CPD) was 99.999% by including the 10 microsatellites loci individual identification system. And then matching probability in that two different individuals incidentally have same genotype was estimated to $0.36{\times}10^{-7}$. The system employing the 10 markers therefore provided to be applicable to individual identification in Korea native chicken.

• Journal of Life Science
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• v.24 no.8
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• pp.910-914
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• 2014

For the identification of the Jeju black cattle, Hanwoo and imported beef, we performed a multiplex polymerase chain reaction (PCR) associated with microsatellite (MS) and melanocortin 1 receptor (MC1R) gene. The MC1R gene plays an important role in regulation of the melanin synthesis within mammalian melanocytes. MC1R encoded by extension (E) locus was almost fixed with recessive red e allele in the Hanwoo. We estimated that the specific genotypes ($E^+/E^+$, $E^+/e$) of MC1R gene were characteristic genotypes of Jeju black cattle. But the PCR products resulted from using the MC1R gene derived primers only are not sufficient to identify Jeju black cattle from other relatives. We performed two times of successive multiplex PCR to provide a more accurate result for the identification of Jeju black cattle. The results suggest that two types of successive multiplex PCR methods using MC1R gene and Microsatellite derived primer set will be more useful to identification of Jeju black cattle, Hanwoo and imported beef.

• Genomics & Informatics
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• v.16 no.1
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• pp.10-13
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• 2018

Until now microsatellite (MS) have been a popular choice of markers for parentage verification. Recently many countries have moved or are in process of moving from MS markers to single nucleotide polymorphism (SNP) markers for parentage testing. FAO-ISAG has also come up with a panel of 200 SNPs to replace the use of MS markers in parentage verification. However, in many countries most of the animals were genotyped by MS markers till now and the sudden shift to SNP markers will render the data of those animals useless. As National Institute of Animal Science in South Korea plans to move from standard ISAG recommended MS markers to SNPs, it faces the dilemma of exclusion of old animals that were genotyped by MS markers. Thus to facilitate this shift from MS to SNPs, such that the existing animals with MS data could still be used for parentage verification, this study was performed. In the current study we performed imputation of MS markers from the SNPs in the 500-kb region of the MS marker on either side. This method will provide an easy option for the labs to combine the data from the old and the current set of animals. It will be a cost efficient replacement of genotyping with the additional markers. We used 1,480 Hanwoo animals with both the MS data and SNP data to impute in the validation animals. We also compared the imputation accuracy between BovineSNP50 and BovineHD BeadChip. In our study the genotype concordance of 40% and 43% was observed in the BovineSNP50 and BovineHD BeadChip respectively.

• Reproductive and Developmental Biology
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• v.37 no.4
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• pp.205-211
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• 2013

The swine is one of the most widespread mammalian throughout the whole world. Presently, many studies concerning microsatellites in swine, especially domestic pigs, have been carried out in order to investigate general diversity patterns among either populations or breeds. Until now, a lot of time and effort spend into a single PCR method. But simple and more rapid multiplex PCR methods have been developed. The purpose of this study is to develop a robust set of microsatellites markers (MS marker) for traceability and individual identification. Using multiplex-PCR method with 23 MS marker divided 2 set, various alleles occurring to 5 swine breed (Berkshire, Landrace, Yorkshire, Duroc and Korea native pig) used markers to determine allele frequency and heterozygosity. MS marker found 4 alleles at SW403, S0227, SWR414, SW1041 and SW1377. The most were found 10 alleles at SW1920. Heterozygosity represented the lowest value of 0.102 at SWR414 and highest value of 0.861 at SW1920. So, it was recognized appropriate allele frequency for individual identification in swine. Using multiplex-PCR method, MS markers used to determine individual identification biomarker and breed-specific marker for faster, more accurate and lower analysis cost. Based on this result, a scientific basis was established to the existing pedigree data by applying genetics additionally. Swine traceability is expected to be very useful system and be conducted nationwide in future.

• Bulletin of the Korean Chemical Society
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• v.30 no.11
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• pp.2655-2660
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• 2009

A breed of cattle, i.e., Korean cattle (Hanwoo), was identified based on the DNA mobilities of their microsatellites (MSs) by capillary gel electrophoresis (CGE) with a laser-induced fluorescence (LIF) detector. The MS markers were used for the accurate identification of species-specific genes. The DNA mobilities of the MS markers of Hanwoo and Holstein were measured using a CGE system with a fused-silica capillary (inner diameter of 75 ${\mu}m$, outer diameter of 365 ${\mu}m$, and total length of 50 cm). The capillary was dynamically coated with 1.0% (w/v) polyvinylpyrrolidone ($M_r$ = 1,000,000) and then filled with a mixture of 1.3% (w/v) poly(ethylene oxide) ($M_r$ = 600,000) and 1.9% (w/v) poly(ethylene oxide) (Mr = 8,000,000) as a sieving gel matrix. The species-specific genes of Hanwoo and Holstein were clearly distinguished within 33 min. This CGE assay technique is expected to be a useful analytical method for the fast and accurate identification of breeds of cattle.

• Korean Journal of Poultry Science
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• v.44 no.2
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• pp.75-81
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• 2017

A total of 340 individuals from seven duck populations were studied using 24 polymorphic microsatellite (MS) markers to identify plumage colors with genetic diversity. The estimated average number of alleles (Na), polymorphic information content (PIC) value, and expected heterozygosity (He) per locus of all populations were 11.5, 0.602, and 0.635, respectively. The calculated population genetic distance (Fst), inbreeding coefficient of individuals within duck populations (Fis), and total inbreeding among populations (Fit) were 0.135, 0.105, and 0.229, respectively. Statistical analyses for each population using 24 marker combinations, revealed that the estimated average number of effective alleles (Ne), observed heterozygosity (Ho), and fixation index of inbreeding within populations (F) were 3.129, 0.505, and 0.104, respectively. The results of genetic distance and phylogenetic analysis revealed that Korean native duck populations were clearly separated from all Bangladeshi duck populations. Moreover, all populations clustered well according to their genetic distance, but could not be clearly separated according to black and white plumage colors or plumage color pattern. The combination of these 24 MS markers can be used for discrimination and determination of the genetic diversity of native duck breeds in further investigations for conservation and special development purposes.

• Journal of Animal Reproduction and Biotechnology
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• v.36 no.3
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• pp.154-161
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• 2021

A number of Korean Chicken breeds were registered in Domestic Animal Diversity Information System (DAD-IS, http://dad.fao.org/) of the Food and Agriculture Organization (FAO). Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. Therefore, this study aimed to analysis the genetic diversity and relationship of 22 Korean Chicken breeds using 12 microsatellite (MS) markers. The mean number of alleles for each variety was 5.52, ranging from a 3.75 (Leghorn F; NF) to a 7.0 (Ross). The most diverse breed was the Hanhyup3 (HCC), which had the highest expected heterozygosity (H_Exp) (0.754) and polymorphic information content (PIC) (0.711). The NF was the least diverse population, having the lowest H_Exp (0.467) and PIC (0.413). As a result of the principal coordinates analysis (PCoA) and factorial correspondence analysis (FCA) confirmed that Hy-line Brown (HL) and Lohmann Brown (LO) are very close to each other and that Leghorn and Rhode Island Red (RIR) are clearly distinguished from other groups. Thus, the reliability and power of identification using 12 types of MS markers were improved, and the genetic diversity and probability of individual discrimination were confirmed through statistical analysis. This study is expected to be used as basic data for the identification of Korean chicken breeds, and our results indicated that these multiplex PCR marker sets will have considerable applications in population genetic structure analysis.