• Horticultural Science & Technology
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• v.33 no.5
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• pp.737-750
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• 2015

This study was carried out to construct a DNA profile database for 102 watermelon cultivars through the comparison of polymorphism level and genetic relatedness using genomic microsatellite (gMS) and expressed sequence tag (EST)-microsatellite (eMS) markers. Sixteen gMS and 10 eMS primers showed hyper-variability and were able to represent the genetic variation within 102 watermelon cultivars. With gMS markers, an average of 3.63 alleles per marker were detected with a polymorphism information content (PIC) value of 0.479, whereas with eMS markers, the average number of alleles per marker was 2.50 and the PIC value was 0.425, indicating that eMS detects a lower polymorphism level compared to gMS. Cluster analysis and Jaccard's genetic distance coefficients using the unweighted pair group method with arithmetic average (UPGMA) based on the gMS, eMS, and combined data sets showed that 102 commercial watermelon cultivars could be categorized into 6 to 8 major groups corresponding to phenotypic traits. Moreover, this method was sufficient to identify 78 out of 102 cultivars. Correlation analysis with Mantel tests for those clusters using 3 data sets showed high correlation ($r{\geq}0.80$). Therefore, the microsatellite markers used in this study may serve as a useful tool for germplasm evaluation, genetic purity assessment, and fingerprinting of watermelon cultivars.

• Journal of fish pathology
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• v.34 no.1
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• pp.9-15
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• 2021

Rock bream (Oplegnathus fasciatus) is a highly valued aquaculture species in Korea. However, the aquaculture industry suffers huge economic losses due to rock bream iridovirus (RBIV) infection in summer. The objective of this study was to determine genetic diversity and relationships of DNAs isolated from two groups of rock bream after RBIV infection using five microsatellite (MS) markers. The first group of fish died early and the second group of fish died later after RBIV infection. In this experiment, 90 fish (5.1±1.0 cm and 4.1±1.3 g) were injected with 50 μl of RBIV (10⁴ TCID⁵⁰/ml) and maintained at 26℃ for 15 days. Genomic DNAs were extracted from fins of 20 fish that died earlier or later after RBIV infection. These DNAs were subjected to genotyping using five MS markers (CA-03, CA3-05, CA3-06, CA-10, and CA3-36). Of these markers, CA3-05 (early death group), CA3-06 (late death group), and CA3-36 (both early and late death groups) showed different alleles distribution rates. In-depth studies are needed to provide valuable information for selecting RBIV-resistant fish. In conclusion, microsatellite marker distribution pattern differences between early- and late- death groups of rock bream after RBIV infection showing different RBIV susceptibilities were determined using MS markers and genotyping. Results of this study suggest that MS markers could be used to facilitate the selection of RBIV resistant rock bream.

• Food Science of Animal Resources
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• v.25 no.1
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• pp.26-31
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• 2005

Leptin, the product of the obesity (ob) gene, is synthesized in adipocytes or fat cells and has been implicated in the regulation of food intake, energy balance and body composition in mammals. Therefore, the leptin gene could be a candidate gene controlling fat deposition, meat quality and carcass traits in cattle. In this study the microsatellite genotypes for leptin gene were determined and their effects on carcass traits and meat quality were estimated in Korean cattle. Six different microsatellite alleles within leptin gene were identified and gene frequencies of 173, 177, 184, 186, 190 and 192 bp alleles were 0.012, 0.308, 0.067, 0.260, 0.342 and 0.016, respectively. The microsatellite marker of the leptin gene showed a significant association with the carcass percentage (CP) and marbling score (MS). Animals with genotypes 192/192 and 177/184 had higher CP than animals with other genotypes. Animals with genotypes 184/192 and 177/184 had higher MS compared with animals with other genotypes. Thus, the results suggest that the 177, 184 and 192 bp alleles may be associated with increased carcass percentage and intramuscular fat levels. No associations were found between the microsatellite genotypes of the leptin gene and other carcass traits such as carcass weight (CW), backfat thickness (BF) and M. longissimus dorsi area (LDA). In conclusion, the microsatellite markers of the leptin gene may be useful for marker-assisted selection of carcass traits and meat quality in Korean cattle.

• Journal of Life Science
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• v.30 no.10
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• pp.912-918
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• 2020

The Korean native black goat (Capra hircus coreanae) is the goat species to be officially registered in Korea under the Food and Agriculture Organization. The object of this study is to establish a set of microsatellite (MS) markers for the individual identification and parentage verification of goats. In this study, we analyzed alleles of MS markers in crosses between Korean native black goats and crossbred goats (n=304 animals), and, based on the diversity of alleles for each marker, we selected 11 MS markers for individual identification and parentage verification. Using these 11 MS markers, the probabilities of different individuals with the same genotype being found within random and half-sib mating populations were 5.58×10^-10 and 1.15×10^-7, respectively. The parentage verification accuracy was 0.999996 when information about the parents was available and 0.999833 with no information. Thus, even given the total rearing population of 576,150 animals in South Korea, we concluded that these markers could be used for the individual identification and parentage verification of goats. Moreover, by analyzing the genetic relationships between the four lines of Korean native black goats and the crossbred goats, we verified the genetic characteristics of Korean native black goats, confirming their conservation value as a unique genetic resource.

• Food Science of Animal Resources
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• v.34 no.6
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• pp.763-768
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• 2014

The identity of 45 Hanwo and 47 imported beef (non-Hanwoo) samples from USA and Australia were verified using the microsatellite (MS) marker and single nucleotide polymorphism (SNP) methods. Samples were collected from 19 supermarkets located in the city of Seoul and Gyeonggi province, South Korea, from 2009 to 2011. As a result, we obtained a 100% concordance rate between the MS and SNP methods for identifying Hanwoo and non-Hanwoo beef. The MS method presented a 95% higher individual discriminating value for Hanwoo (97.8%) than for non-Hanwoo (61.7%) beef. For further comparison of the MS and SNP methods, blood samples were collected and tested from 54 Hanwoo ${\times}$ Holstein crossbred cattle (first, second, and third generations). By using the SNP and MS methods, we correctly identified all of the first-generation crossbred cattle as non-Hanwoo; in addition, among the second and third generation crossbreds, the ratio identified as Hanwoo was 20% and 10%, respectively. The MS method used in our study provides more information, but requires sophisticated techniques during each experimental process. By contrast, the SNP method is simple and has a lower error rate. Our results suggest that the MS and SNP methods are useful for discriminating Hanwoo from non-Hanwoo breeds.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.10
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• pp.1329-1333
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• 2004

To isolate the microsatellites from the chromosomal DNA of the Korean cattle (Hanwoo) and to use those for the genetic selection, four bacteriophage genomic libraries containing the chromosomal DNA of six Hanwoo steers showing the differences in meat quality and quantity were used. Screening of the genomic libraries using $^{32}P-radiolabeled 5'-({CA})_{12}-3$nucleotide as a probe, resulted in isolation of about 3,000 positive candidate bacteriophage clones that contain $(CA)_n$-type dinucleotide microsatellites. After confirming the presence of microsatellite in each positive candidate clone by Southern blot analysis, the DNA fragments that include microsatellite and flanking sequences possessing less than 2 kb in size, were subcloned into plasmid vector. Results from the analysis of microsatellite length polymorphism, using twenty-two PCR primers designed from flanking region of each microsatellite DNA, demonstrated that 208 and 210 alleles of HW-YU-MS#3 were closely related to the economic traits such as marbling score, daily gain, backfat thickness and M. longissimus dorsi area in Hanwoo. Interestingly, HW-YU-MS#3 microsatellite was localized in bovine chromosome 17 on which QTLs related to regulation of the body fat content and muscle ypertrophy locus are previously known to exist. Taken together, the results from the present study suggest the possible use of the two alleles as a DNA marker related to economic trait to select the Hanwoo in the future.

• Fisheries and Aquatic Sciences
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• v.10 no.4
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• pp.186-190
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• 2007

We examined the genetic variability of Asian chum salmon (Oncorhynchus keta) populations using nuclear microsatellite (ms) DNA analysis with four polymorphic loci (OKM4, OKM5, OKM7, and OKM8) in 397 individuals from nine populations, including one in Korea, seven in Japan, and one in Russia. The msDNA gene diversity was highest in the Japanese populations, suggesting greater genetic variation in the populations in Japan than in populations in Korea and Russia. The pairwise $F_{ST}$ estimates based on our msDNA data showed that the Korean population was genetically different from the Japanese and Russian populations, and there were higher $F_{ST}$ estimates between Hokkaido and Honshu populations than between other population pairs. A neighbor-joining tree showed that the Korean population was distinct from two other clusters, representing the populations in Honshu and the populations in Hokkaido and Russia. These results suggest that the observed population genetic patterns of Asian chum salmon might be influenced by low or restricted gene flow.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.4
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• pp.471-478
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• 2016

Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.

• Journal of Animal Science and Technology
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• v.52 no.6
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• pp.451-457
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• 2010

The porcine MHC (Major Histocompatibility Complex), encoding the SLA (Swine Leukocyte Antigen) genes, is one of the most significant regions associated with immune rejection in relation to transplantation. In this study, three SLA class I (SLA-1, SLA-3, SLA-2) loci and three SLA class II (DRB1, DQB1, DQA) loci were investigated in the previously unidentified Korean native pig (KNP) population that was closely inbred in the Livestock Technology Research Station in Cheongyang, Korea. Total thirteen KNPs from four generations were genotyped for the SLA alleles and haplotypes were investigated using PCR-SSP (Sequence-Specific Primer) method. The results showed that all of these KNPs had Lr-56.30/56.30 homozygous haplotype, indicating high level of inbreeding in the SLA genes. The inbreeding status of these animals was also investigated using microsatellite (MS) markers. From the 50 MS markers investigated, 17 MS markers were fixed in all generations and the fixed alleles are increased as 26 loci for the fourth generation. Two MS markers, S0069 and SW173, were heterozygous for all the animals tested. Observed and expected heterozygosities were calculated and the average inbreeding coefficients for each generation were also calculated. In the fourth generation, the average inbreeding coefficients was 0.732 and this may increase with further inbreeding process. Analysis of the SLA haplotypes and MS alleles can give important information for breeding the pigs for xenotransplantation studies.

• Journal of Animal Science and Technology
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• v.51 no.5
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• pp.353-360
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• 2009

When 14 microsatellite (MS) markers were applied in the identifying test for 480 Hanwoo, the discriminating power was estimated as $3.43{\times}10^{-27}$ based on the assumption of a random mating group (PI). This rate is 1,000 times higher than that of 60 single nucleotide polymorphism (SNP) markers. On the other hand, the power of the 60 SNP markers was estimated as $4.69{\times}10^{-20}$ and $8.02{\times}10^{-12}$ on the assumption of a half-sib mating group ($PI_{half-sibs}$) and a full-sib mating group ($PI_{sibs}$), respectively. These powers were 10 times and 10,000 times higher than those of the 14 MS markers. The results indicated that the total number of alleles (MS vs SNP = 146 vs 120) acted as a key factor for the discriminating power in a random mating population, and the total number of markers (MS vs SNP = 14 vs 60) was a dominant influence on the power in half-sib and full-sib populations. In the Hanwoo population, in which it was assumed that the entire population is the enormous half-sib group formed by the absolute genetic contribution of a few nuclear bulls, there will be only a 10 times difference in the discriminating power between the 14 MS markers and the 60 SNP makers. However, the probability of not excluding a candidate parent pair from the parentage of an arbitrary offspring, given that only the genotype of the offspring ($PNE_{pp}$) was 1,000 times higher as shown by the 14 MS markers than that by the 60 SNP markers. The strong points of SNP makers are the stability of the variation (low mutation rate) and automation of high-throughput genotyping. In order to apply these merits for the practical and constant Hanwoo identity test, research and development are required to set a cost-effective platform and produce a homemade apparatus for SNP genotyping.