• Horticultural Science & Technology
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• v.30 no.3
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• pp.278-285
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• 2012

Cymbidium goeringii is one of the most important and popular species in the orchid family in north-east Asia. In the present study, we prepared multiplex PCR system, and used it for the genotyping of eight simple sequence repeats (SSR) markers (CG409, CG415, CG709, CG722, CG787, CG1023, CG1210, and CG1281) in subject with 40 samples of cultivated varieties. All the analyzed samples showed different combined genotypes. The average combined power of discrimination was very high value of $7.14{\times}10^{-10}$, and observed heterozygosity (Ho = 0.466) was similar with two wild populations of C. goeringii, which may indicate no or little occurrence of genetic change after collection from wild habitats. The present study also developed a two-dimensional barcode to express information of genotype results of eight SSR markers (SSR DNA ID). The discrimination power of DNA ID between two individuals will be statistically more than 99.999999%. The SSR DNA ID and two-dimensional barcode may be very usefully applied for the discrimination and maintence of cultivars of C. goeringii.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.3
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• pp.323-333
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• 2013

This study investigated the geographic and pairwise distances of nine Chinese local Cashmere goat populations through the analysis of 20 microsatellite DNA markers. Fluorescence PCR was used to identify the markers, which were selected based on their significance as identified by the Food and Agriculture Organization of the United Nations (FAO) and the International Society for Animal Genetics (ISAG). In total, 206 alleles were detected; the average allele number was 10.30; the polymorphism information content of loci ranged from 0.5213 to 0.7582; the number of effective alleles ranged from 4.0484 to 4.6178; the observed heterozygosity was from 0.5023 to 0.5602 for the practical sample; the expected heterozygosity ranged from 0.5783 to 0.6464; and Allelic richness ranged from 4.7551 to 8.0693. These results indicated that Chinese Cashmere goat populations exhibited rich genetic diversity. Further, the Wright's F-statistics of subpopulation within total (FST) was 0.1184; the genetic differentiation coefficient (GST) was 0.0940; and the average gene flow (Nm) was 2.0415. All pairwise FST values among the populations were highly significant (p<0.01 or p<0.001), suggesting that the populations studied should all be considered to be separate breeds. Finally, the clustering analysis divided the Chinese Cashmere goat populations into at least four clusters, with the Hexi and Yashan goat populations alone in one cluster. These results have provided useful, practical, and important information for the future of Chinese Cashmere goat breeding.

• Journal of Life Science
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• v.20 no.7
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• pp.1086-1092
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• 2010

To estimate the genetic characteristics and cumulative power of discrimination (CPD) within Korean native commercial chicken, we used a total of 395 genomic DNAs from six breeds population (Korean Native Red chicken: R, Korean Native Yellow chicken: Y, Korean native Commercial Chicken: C, Ogal chicken: S, Hy-Line Brown: H, White Leghorn: W). Genetic diversity indices including mean allele number among loci, unbiased heterozygosity ($h_i$) within locus, effective number of alleles ($N_e$) and polymorphism information content (PIC) as well as the unbiased average heterozygosity (H) among loci in the populations were calculated using the generated allele frequencies by each marker. Frequencies of microsatellites markers were used to estimate heterozygosities and genetic distances. The nearest distance (0.119) was observed between the C and Y strains. The generated unbiased average heterozygosity among loci in each population was integrated to the global formula of CPD and the result demonstrated that the CPD within the six chicken populations was 99.461%.

• Journal of Mushroom
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• v.19 no.1
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• pp.76-80
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• 2021

To develop a method for the differentiation of Pleurotus ostratus cultivars, the multiplex-simple sequence repeat (SSR) primer set based on the SSRs obtained from whole genomic DNA sequence analysis was designed with two polymerase chain reaction (PCR) primer sets. These SSR primer sets were employed to distinguish 10 cultivars and strains. Twenty polymorphic markers were selected based on the genotyping results. PCR with each primer produced 1-4 distinct bands ranging in size from 150 to 350 bp, which was within the expected range. However, since a sole SSR marker was unable to detect polymorphisms in every cultivar, multiplex PCRs with composite PCR primer sets were employed. The multiplex primer, "166+115," completely discriminated 12 cultivars and strains with 40 loci, which were 12 more than the simple arithmetic addition of each locus of the primers 115 and 166. These results might be useful to provide an efficient method for the differentiation of P. ostreatus cultivars with separate PCRs for the quality control of spawn and protection of breeders' rights.

• Journal of Korean Society of Forest Science
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• v.112 no.1
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• pp.40-56
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• 2023

Tree species within the Populus genus grow rapidly and have an excellent capacity to absorb carbon, conferring substantial ability to effective purify the environment. Poplar breeding can be achieved rapidly and efficiently if a genetic linkage map is constructed and quantitative trait loci (QTLs) are identified. Here, a high-density genetic linkage map was constructed for the control pollinated progeny using the genotyping-by-sequencing (GBS) technique, which is a next-generation sequencing method. A search was also performed for the genes associated with quantitative traits located in the genetic linkage map by examining the variables of height and diameter at root collar, and resilience to insect damage. The height and diameter at root collar were measured directly, while the ability to recover from insect damage was scored in a 4-year-old breeding population of aspen hybrids (Odae19 × Bonghyeon4 F1) established in the research forest of Seoul National University. After DNA extraction, paternity was confirmed using five microsatellite markers, and only the individuals for which paternity was confirmed were used for the analysis. The DNA was cut using restriction enzymes and the obtained DNA fragments were prepared using a GBS library and sequenced. The analyzed results were sorted using Populus trichocarpa as a reference genome. Overall, 58,040 aligned single-nucleotide polymorphism (SNP) markers were identified, 17,755 of which were used for mapping genetic linkages. The genetic linkage map was divided into 19 linkage groups, with a total length of 2,129.54 cM. The analysis failed to identify any growth-related QTLs, but a gene assumed to be related to recovery from insect damage was identified on linkage group (chromosome) 4 through genome-wide association study.

• Korean Journal of Poultry Science
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• v.46 no.2
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• pp.65-75
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• 2019

A number of Korean native chicken(KNC) populations were registered in FAO (Food and Agriculture Organization) DAD-IS (Domestic Animal Diversity Information Systems, http://www.fao.org/dad-is). But there is a lack of scientific basis to prove that they are unique population of Korea. For this reason, this study was conducted to prove KNC's uniqueness using 25 Microsatellite markers. A total of 548 chickens from 11 KNC populations (KNG, KNB, KNR, KNW, KNY, KNO, HIC, HYD, HBC, JJC, LTC) and 7 introduced populations (ARA: Araucana, RRC and RRD: Rhode Island Red C and D, LGF and LGK: White Leghorn F and K, COS and COH: Cornish brown and Cornish black) were used. Allele size per locus was decided using GeneMapper Software (v 5.0). A total of 195 alleles were observed and the range was 3 to 14 per locus. The MNA, $H_{\exp}$, $H_{obs}$, PIC value within population were the highest in KNY (4.60, 0.627, 0.648, 0.563 respectively) and the lowest in HYD (1.84, 0.297, 0.286, 0.236 respectively). The results of genetic uniformity analysis suggested 15 cluster (${\Delta}K=66.22$). Excluding JJC, the others were grouped in certain cluster with high genetic uniformity. JJC was not grouped in certain cluster but grouped in cluster 2 (44.3%), cluster 3 (17.7%) and cluster8 (19.1%). As a results of this study, we can secure a scientific basis about KNC's uniqueness and these results can be use to basic data for the genetic evaluation and management of KNC breeds.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.17 no.4
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• pp.292-302
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• 2012

This paper reviews comparison analysis of current and latest application for stock identification methods of Todarodes pacificus, and the pros and cons of each method and consideration of how to compensate for each other. Todarodes pacificus which migrates wide areas in western North Pacific is important fishery resource ecologically and commercially. Todarodes pacificus is also considered as 'biological indicator' of ocean environmental changes. And changes in its short and long term catch and distribution area occur along with environmental changes. For example, while the catch of pollack, a cold water fish, has dramatically decreased until today after the climate regime shift in 1987/1988, the catch of Todarodes pacificus has been dramatically increased. Regarding the decrease in pollack catch, overfishing and climate changes were considered as the main causes, but there has been no definite reason until today. One of the reasons why there is no definite answer is related with no proper analysis about ecological and environmental aspects based on stock identification. Subpopulation is a group sharing the same gene pool through sexual reproduction process within limited boundaries having similar ecological characteristics. Each individual with same stock might be affected by different environment in temporal and spatial during the process of spawning, recruitment and then reproduction. Thereby, accurate stock analysis about the species can play an efficient alternative to comply with effective resource management and rapid changes. Four main stock analysis were applied to Todarodes pacificus: Morphologic Method, Ecological Method, Tagging Method, Genetic Method. Ecological method is studies for analysis of differences in spawning grounds by analysing the individual ecological change, distribution, migration status, parasitic state of parasite, kinds of parasite and parasite infection rate etc. Currently the method has been studying lively can identify the group in the similar environment. However It is difficult to know to identify the same genetic group in each other. Tagging Method is direct method. It can analyse cohort's migration, distribution and location of spawning, but it is very difficult to recapture tagged squids and hard to tag juveniles. Genetic method, which is for useful fishery resource stock analysis has provided the basic information regarding resource management study. Genetic method for stock analysis is determined according to markers' sensitivity and need to select high multiform of genetic markers. For stock identification, isozyme multiform has been used for genetic markers. Recently there is increase in use of makers with high range variability among DNA sequencing like mitochondria, microsatellite. Even the current morphologic method, tagging method and ecological method played important rolls through finding Todarodes pacificus' life cycle, migration route and changes in spawning grounds, it is still difficult to analyze the stock of Todarodes pacificus as those are distributed in difference seas. Lately, by taking advantages of each stock analysis method, more complicated method is being applied. If based on such analysis and genetic method for improvement are played, there will be much advance in management system for the resource fluctuation of Todarodes pacificus.

• Clinical and Experimental Reproductive Medicine
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• v.32 no.1
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• pp.17-26
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• 2005

Objective: Preimplantation genetic diagnosis (PGD) is reserved for couples with a risk of transmitting a serious and incurable disease, and hence avoids the undesirable therapeutic abortion. In this study, we evaluated the efficacy of PGD for Duchenne muscular dystrophy (DMD) cases by the fluorescent PCR with polymorphic linked markers and the conventional duplex-nested PCR methods. Methods: Biopsy of one or two blastomeres was done from the embryos fertilized by ICSI on the third day after fertilization. We performed two cases of PGD-DMD by the duplex-nested PCR for the causative mutation loci and the SRY gene on Y chromosome. The triplex fluorescent PCR for the mutation loci, the SRY gene and the polymorphic microsatellite marker on X chromosome was applied for two cases of PGD-DMD. Results: By the duplex-nested PCR, successful diagnosis rate was 95.5% (21/22), but we could not discriminate the female embryos whether normal or carrier in this X-linked recessive disease. However, the triplex fluorescent PCR method showed 100% (27/27) of successful diagnosis rate, and all female embryos (n=17) were distinguished normal (n=10) from carrier (n=7) embryos. Unaffected and normal embryos were transferred into mother's uterus after diagnosis. A healthy normal male was achieved after PGD with the duplex-nested PCR method and a twin, a male and a female, were delivered with triplex fluorescent PCR method. The normality of dystrophin gene was confirmed by amniocentesis and postnatal genetic analysis in all offsprings. Conclusion: The fluorescent PCR with polymorphic marker might be useful in improving the specificity and reliability of PGD for single gene disorders.

• Journal of Korean Society of Forest Science
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• v.106 no.4
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• pp.417-423
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• 2017

To provide a ecological restoration strategy considering genetic diversity of Abies koreana in Mt. Jiri, the genetic diversity and the genetic differentiation among sub-populations such as Banyabong, Byeoksoryeong, and Cheonwangbong were investigated. The average number of alleles (A) was 7.8, the average number of effective alleles ($A_e$) was 4.9, observed heterozygosity ($H_o$) was 0.578, and expected heterozygosity ($H_e$) was 0.672, respectively. The level of genetic diversity within sub-populations ($H_e=0.672$) was lower than those of both population ($H_e=0.778$) and species ($H_e=0.759$) level. However, the level of genetic diversity was high compared those of Genus Abies. Genetic differentiation was 0.014 from F-statistics ($F_{ST}$) and was 0.004 from AMOVA analysis (${\Phi}_{ST}$). There was no almost genetic differentiation among sub-populations in Mt. Jiri from bayesian clustering. Therefore, If the seeds are sampled sufficiently by selecting the parameters from three sub-populations, it is possible that we could obtain genetically appropriate materials for ecological restoration.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.8
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• pp.1078-1084
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• 2009

The Jindo dog is a Korean natural monument and is recognized by the Fédération Cynologique Internationale. A prominent feature is the diverse coat color within the breed. To analyze the genetic basis of variation in the Jindo coat color, we sequenced the protein-coding regions of the melanocortin 1 receptor gene (MC1R). The MC1R coding sequence was determined from 154 dogs in five breeds (Jindo, Labrador Retriever, English Springer Spaniel, Belgian Malinois, and German Shepherd). To confirm the genetic structure of sampled populations, we tested for Hardy-Weinberg equilibrium (HWE) and computed $F_{st}$ The sample populations did not significantly deviate from HWE. $F_{st}$ was 0.02 between white and fawn Jindo dogs; this was lower than $F_{st}$ between breeds. Six single nucleotide polymorphisms (SNPs) were detected in the MC1R coding region. Among the six SNPs, five were non-synonymous (S90G, T105A, Q159P, M264V, and R306ter) and one was synonymous SNP (Y298Y). From the SNPs, we predicted four haplotypes (H1, H2, H3, and H4) for Jindo MC1R. Jindo dogs had different haplotypes corresponding to different coat colors. H1 was frequently observed in white Jindo dogs with an odds ratio of 5.03 (95% CI: 2.27-11.18, p<0.0001), whereas H2 and H4 were observed only in fawn Jindo dogs. Our findings indicate that SNP haplotype can influence coat color. Knowledge of MC1R haplotypes can help discriminate white and fawn coats in Jindo dogs. We hope this report will trigger more research into the genetics of this traditional Korean dog and will be a reference for dogs of Asian origin. Also, our results will provide a useful genetic marker for Jindo dog breeders who have selected for specific colors.