• Journal of Animal Science and Technology
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• v.50 no.5
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• pp.633-640
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• 2008

With a double mismatch primer set designed for amplifying the modified DNA sequence fragments, bovine melanocortin-1 receptor(MC1R) gene encoded in Extension locus which plays a critical role in coat color development was analyzed using polymerase chain reaction mediated restriction fragment length polymorphism(PCR-RFLP). Amplified PCR fragments were successfully discriminated with combining the MspI- and AluI-RFLP into three major alleles(ED, E+, and e), directly related to bovine coat color phenotypes. The genotyping results showed that Jeju black cattle contained three MC1R alleles, but yellowish-red colored Hanwoo and bridle colored Korean Brindle cattle did not contained the dominant black allele ED. However, two dominant black-colored cattle breeds, Holstein and Angus, contained the ED allele over 96% in frequency. Hanwoo×Holstein F1 and Hanwoo×Angus F1 crossbred calves showed ED/e MC1R genotypes, and uniformly black coat color. the results suggested that this MC1R genotyping method be useful in allele discrimination for bovine MC1R gene which used for breed classification and characterization, as one of the important genetic markers, using combination of MspI- and AluI-RFLP for modified PCR product amplified with a newly designed double mismatch primer set.

• Journal of Animal Science and Technology
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• v.55 no.2
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• pp.87-93
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• 2013

We identified four new bovine tri-nucleotide microsatellite loci and analyzed their sequence structures and genetic parameters in 105 randomly selected Korean cattle (Hanwoo). Allele numbers of the loci B17S0808, B15S6253, B8S7996, and B17S4998 were 10, 11, 12, and 29, respectively. These alleles contained a simple or compound repeat sequences with some variations. Allele distributions of all these loci were in Hardy-Weinberg equilibrium (P > 0.05). Observed heterozygosity and expected heterozygosity ranged from 0.54 (B15S6253) to 0.92 (B17S4998) and from 0.599 (B15S6253) to 0.968 (B17S4998), respectively, and two measures of heterozygosity at each locus were highly correlated. Polymorphism information content (PIC) for these 4 loci ranged from 0.551 (B15S6253) to 0.932 (B17S4998), which means that all these loci are highly informative (PIC > 0.5). Other genetic parameters, power of discrimination (PD) and probability of exclusion (PE) ranged from 0.783 (B15S6253) to 0.984 (B17S4998) and from 0.210 (B15S6253) to 0.782 (B17S4998), respectively. Their combined PD and PE values were 0.9999968 and 0.98005176, respectively. Capillary electrophoresis revealed that average peak height ratio for a stutter was 13.89% at B17S0808, 26.67% at B15S6253, 9.09% at B8S7996, and 43.75% at B17S4998. Although the degree of genetic variability of the locus B15S6253 was relatively low among these four microsatellite markers, their favorable parameters and low peak height ratios for stutters indicate that these four new tri-nucleotide microsatellite loci could be useful multiplex PCR markers for the forensic and population genetic studies in cattle including Korean native breed.

• 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.

• Korean Journal of Poultry Science
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• v.42 no.1
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• pp.1-8
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• 2015

Recently, duck meat consumption has been rapidly increased because consumers recognized duck meat for healthy food. In relation to this, Korean duck industry need to develop Korean native duck (KND) breed for both conservation perspective and self-sufficient of the breeding stocks. In this study, 24 microsatellite (MS) markers were investigated for classification of KND and commercial duck (CD) breeds in the Korean market. Using these MS markers, the calculated number of alleles (K), expected heterozygosity (He) values and polymorphic information contents (PIC) were 1~16, 0~0.865 and 0~0.841, respectively. Also, the expected probability of identical values in random individuals (PI), random sib ($PI_{sib}$) and random half-sib ($PI_{half-sib}$) were estimated as $1.64{\times}10^{-16}$, $2.60{\times}10^{-7}$ and $1.30{\times}10^{-12}$, respectively. The results indicated that the expected probabilities of identity powers were enough for the individual identification. However, KND and CD breeds were not fully discriminated well using the 24 MS markers, which may CD and KND has shared same origin or crossbred. Therefore, further studies will be ultimately needed for developing a genetically pure line of KND breed even though the DNA markers used. Finally, these results will provide useful information for individual traceability system in ducks.

• Journal of the Korean Chemical Society
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• v.53 no.6
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• pp.742-748
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• 2009

In the meat industry, correct breed information in food labeling is required to assure meat quality. Genetic markers provide corroborating evidence to identify breed. We described the development of DNA markers to discriminate between Korean beef cattle (Hanwoo), Holstein, and mixed cow beefs. As most breeds are standardized for coat colour, the melanocortin 1 receptor (MC1R) gene, involved in the regulation of eu/pheomelanins synthesis, has been suggested as marker for breed traceability of products of animal origin. We also designed sex-determining region Y (SRY) gene specific primers for Y chromosome detection. In this study, fragments of MC1R gene and SRY gene were amplified by multiplex-PCR and subjected to digestion by MspA1I restriction endonuclease. Reaction products were analysised by denaturing high performance liquid chromatography (DHPLC). As a result, we identified 6 DHPLC peak types from MC1R gene and SRY gene analysis. DHPLC method showed more sensitive than RFLP method for DNA fragments analysis. Therefore, DHPLC method can apply to identify for Hanwoo, Holstein and mixed beef.

• Journal of Food Hygiene and Safety
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• v.13 no.4
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• pp.388-393
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• 1998

Recently there has been an increasing amount of foreign livestock products distributed in the domestic market due to the market opening. Some vicious dealers sell the foreign beef in the trade name of the native beef during the final distribution step to arouse the social criticism frequently. In this report, we investigated a method to distinguish the native beef from the foreign one scientifically using the PCR-RAPD, a recent gene technique. Hygienical safety was also examined using a microbiological test for toxicity of Escherichia coli 0157:H7 and the food poisoning bacteria. The conditions of DNA amplification for the PCR analysis were $1{\times}Taq$ polymerase buffer, 1.5 mM $MgCl_2,\;50\;\mu\textrm{M}$ dNTP, 100 ng primers, 2.5 unit Taq polymerase and 5~20 ng template DNA, with the fmal volume of $50\;\mu\textrm{\ell}$. The size of the amplified product was detected mostly in the range of 0.5~2.0 kbp. The size of DNA, gene marking factor, which could be a criterion distinguishing the native beef from the foreign one, appeared approximately 1.2 kbp. The native beef was distinguished from the foreign beef with more than 90% of confidence by the gene marking factor. This method was expected to be useful in the breed discrimination between the native beef and the foreign one. The hygienical test results showed that, fortunately, neither Salmonella spp. and Listeria monocytogenes which form a principal cause of the food poisoning nor Enterohemorrhagic Escherichia coli : EHEC which have provoked a recent social disturbance, were detected at all.

• Food Science of Animal Resources
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• v.27 no.2
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• pp.150-156
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• 2007

This study was conducted to analyze the genetic characteristics of Korean Native Pigs(KNP), and to establish an individual identification system comprising many microsatellite markers located on different pig autosomes. Genotype data from 13 microsatellites typed in 446 animals was used to determine the validation of a method of individual identification in 4 KNP. A total of 112 alleles of the 13 microsatellites were detected and average heterozygosities(polymorphic information content) ranged from 0.286(0.423) to 0.686(0.796) in this study. Comparing the pattern of allele frequency among the KNP, Yorkshire, Landrace and Duroc breeds, there was specific differentiation between populations at multi-allelic loci. The cumulative power of discrimination(CPD) was 99.999% by including 10 microsatellite loci for the individual identification system. The probability that two different individuals incidentally have same genotype was estimated to be $0.36{\times}10^{-9}$. The system employing these 10 markers therefore proved to be applicable to the individual identification of KNP.

• Journal of The Korean Society of Grassland and Forage Science
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• v.37 no.2
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• pp.168-175
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• 2017

Single nucleotide polymorphisms (SNP) markers allow rapid screening of crop varieties in early growth stages. We developed a modified SNP PCR procedure for assaying SNPs in maize. For SNP marker development, we chosen 200 SNP sites from MaizeGDB database, and designed two base pair mismatch primers based on putative SNP site of B73 genome sequence. PCR products size was from 200 to 500 bp or was not shown in the case of SNP site existing in Korean silage corns. Using previously discovered 16 primer sets, we investigated distinctness of 50 silage F1 hybrid corns including 10 Korean silage corns developed by RDA such as Gangdaok, Kwangpyeongok, Dapyeongok, Andaok, Yanganok, Singwangok, Jangdaok, Cheongdaok, Pyeonggangok, and Pyeonganok as well as 40 foreign commercial silage corns. From cluster analysis, we confirmed that 10 Korean silage F1 hybrid corns were clearly distinguished except for Singwangok, P1395, and several foreign commercial corns, and selected minimum SNP primer combination for Gangdaok, Jangdaok, Pyeonggangok, and Pyeonganok. Therefore, development of SNP marker sets might be faster, cheaper, and feasible breed discrimination method through simple PCR and agarose gel electrophoresis.

• Journal of Animal Science and Technology
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• v.55 no.3
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• pp.185-194
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• 2013

Microsatellite markers have been a useful genetic tool in determining diversity, relationships and individual discrimination studies of livestock. The level of genetic diversity, relationships among two Korean indigenous chicken brand populations (Woorimatdag: WR, Hanhyup3: HH) as well as two pure populations (White Leghorn: WL, Rhode Island Red: RIR) were analyzed, based on 26 MS markers. A total of 191 distinct alleles were observed across the four chicken populations, and 47 (24.6%) of these alleles were unique to only one population. The mean $H_{Exp}$ and PIC were estimated as 0.667 and 0.630. Nei's $D_A$ genetic distance and factorial correspondence analysis (FCA) showed that the four populations represented four distinct groups. However, the genetic distance between each Korean indigenous chicken brand (WR, HH) and the pure population (WL, RIR) were threefold that among the WR and HH. For the STRUCTURE analyses, the most appropriate number of clusters for modeling the data was determined to be three. The expected probabilities of identity among genotypes of random individuals (PI) were calculated as $1.17{\times}10^{-49}$ (All 26 markers) and $1.14{\times}10^{-15}$, $7.33{\times}10^{-20}$ (9, 12 with the highest PI value, respectively). The results indicated that the brand chicken breed traceability system employing the own highest PI value 9 to 12 markers, and might be applicable to individual identification of Korean indigenous chicken brand.