• Journal of Life Science
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• v.15 no.1 s.68
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• pp.45-48
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• 2005

The aim of this study was to construct a correct pedigree of miniature horses (MH). The sex of MH was detected by PCR amplification of the sex determining region of the Y chromosome gene (SRY) prior to parentage testing. Ten random MH samples for parentage testing were genotyped by using 16 micro satellite markers. Since the SRY band (430 bp) was detected in horses No.1, 2, 6, 7, 8, 9, 10, these are male. However, the DNA segment was not identified in horses No.3, 4, and 5, which therefore are female. After genotyping, parentage testing was performed according to Mendelian fashion and International Society for Animal Genetics (ISAG) guideline. Of the 10 MH, 3 were qualified by the compatibility of 16 markers according to Mendelian fashion in the present DNA typing for parentage verification. These results can provide basic information for developing parentage verification and an individual identification system in MH.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.51 no.spc1
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• pp.185-192
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• 2006

This experiment was conducted to assess genetic diversity of waxy corn inbred lines and to identify SSR markers related to major characteristics affected kernel quality for improving waxy corn $F_1$ hybrid with good quality. Diversity of 64 waxy com inbred lines was evaluated using 30 microsatellite markers. The 30 microsatellite markers representing 30 loci in the maize genome detected polymorphisms among the 64 inbred lines and revealed 225 alleles with a mean of 7.5 alleles per primer. The polymorphism Information content (PIC) value ranged from 0.14 to 0.87, with an average of 0.69. Based on Nei's genetic distances, the 64 inbred lines were classified into 9 groups by the cluster analysis. The group I included 26 inbred lines (41%), other groups included 3 to 9 inbred lines. One-way analysis of variance was conducted to identify significant relationship between individual markers and major characteristics that affect kernel quality. The analysis showed that umc1019 was related to amylopectin and crude protein content, me 1020 to amylopectin content and peak viscosity, and bnlg1537 to 100-kernel weight, kernel length, and kernel width.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.12
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• pp.1896-1904
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• 2020

Objective: Estimating the genetic diversity and structures, both within and among chicken breeds, is critical for the identification and conservation of valuable genetic resources. In chickens, microsatellite (MS) marker polymorphisms have previously been widely used to evaluate these distinctions. Our objective was to analyze the genetic diversity and relationships among 22 chicken breeds in Asia based on allelic frequencies. Methods: We used 469 genomic DNA samples from 22 chicken breeds from eight Asian countries (South Korea, KNG, KNB, KNR, KNW, KNY, KNO; Laos, LYO, LCH, LBB, LOU; Indonesia, INK, INS, ING; Vietnam, VTN, VNH; Mongolia, MGN; Kyrgyzstan, KGPS; Nepal, NPS; Sri Lanka, SBC) and three imported breeds (RIR, Rhode Island Red; WLG, White Leghorn; CON, Cornish). Their genetic diversity and phylogenetic relationships were analyzed using 20 MS markers. Results: In total, 193 alleles were observed across all 20 MS markers, and the number of alleles ranged from 3 (MCW0103) to 20 (LEI0192) with a mean of 9.7 overall. The NPS breed had the highest expected heterozygosity (H_exp, 0.718±0.027) and polymorphism information content (PIC, 0.663±0.030). Additionally, the observed heterozygosity (H_obs) was highest in LCH (0.690±0.039), whereas WLG showed the lowest H_exp (0.372±0.055), H_obs (0.384±0.019), and PIC (0.325±0.049). Nei's DA genetic distance was the closest between VTN and VNH (0.086), and farthest between KNG and MGN (0.503). Principal coordinate analysis showed similar results to the phylogenetic analysis, and three axes explained 56.2% of the variance (axis 1, 19.17%; 2, 18.92%; 3, 18.11%). STRUCTURE analysis revealed that the 22 chicken breeds should be divided into 20 clusters, based on the highest ΔK value (46.92). Conclusion: This study provides a basis for future genetic variation studies and the development of conservation strategies for 22 chicken breeds in Asia.

• 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.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.1
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• pp.91-96
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• 2013

Background: p53 alterations have been implicated in the development of many cancers, such as gastric cancer, but there is no evidence of p53 intron alterations in gastritis lesions. The aim of this study was to investigate the p53 intron alterations in gastritis along with p53 and mismatch repair protein expression and microsatellite status. Materials and Methods: PCR-sequencing was conducted for introns 2-7 on DNA extracted from 97 paired samples of gastritis lesions and normal adjacent tissue. Abnormal accumulation of p53 and mismatch repair proteins was investigated using immunohistochemistry. In addition, microsatellite status was evaluated with reference to five mononucleotide markers. Results: Gastritis cases included 41 males and 56 females in the age range of 15-83 years, 87.6% being H.pylori positive. IVS2+38, IVS3ins16 and IVS7+72 were the most polymorphic sites. Their minor allele frequency values were as follows: 0.38, 0.21 and 0.06, respectively. Samples with GG genotype at IVS2+38 and CT at IVS7+72 had no insertion. Moreover, most of the stable samples (91.9 %) had a G allele at IVS2+38. All of the samples were IHC negative for p53 protein, microsatellite stable and expressed mismatch repair proteins. p53 alterations were prominent in the H. Pylori+ group, but without statistical significance. Conclusions: According to our results, some p53 polymorphisms such as IVS2+38, IVS3ins16 and IVS7+72, because of their correlations together or with microsatellite status may contribute to gastritis development. However, so far effects on p53 expression and function remain unclear. Therefore, a comprehensive survey is needed to delineate their biological significance.

• Korean journal of applied entomology
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• v.43 no.4 s.137
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• pp.311-315
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• 2004

The brown planthopper, Nilaparvata lugens, is among the most serious insect pests of rice. It is widely distributed in Asia, Australia and Pacific islands. An earlier mitochondrial DNA study revealed that there exist significant genetic differences between populations north and south of the Red River Delta region in Vietnam. However the mitochondrial DNA was not sufficiently variable to examine the sources of immigration. For a more detailed analysis of geographic population structure of N. lugens, we developed microsatellite markers. Thirty-seven putative microsatellite loci were isolated using a magnetic biotin method, and five primer pairs designed from the flanking regions of sequenced microsatellite clones were labeled with fluorescent. Of these five primer sets, two have proven to be useful across all the samples we used in this study. We used variation at these two microsatellite loci to test the hypothesis that N. lugens biotypes (1, 2, and 3) sampled from laboratory selection constituted distinct genetic units. Allele frequency differences among the three major biotype categories were not significantly different at one locus (27035). However, the other (7314) did show differences among the major three biotypes. The methods we describe here will be useful for studying population structure of crop pest and for tracking the patterns of migratory pest like the rice planthoppers.

• Genomics & Informatics
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• v.7 no.3
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• pp.152-158
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• 2009

Although the genetic basis for bone mineral density (BMD) has been studied by many groups so far, genes responsible for this complex trait has not been completely revealed. In order to localize quantitative trait loci (QTLs) for BMD variation in Asian population, the study was designed using a group of Mongolian population, a genetically closed population with a homogeneous lifestyle. BMD was measured at the left and right wrists and ankles using DEXA in 1,082 participants from 142 families. Genotyping of 13 polymorphic microsatellite markers on chromosome 13 (average spacing 8-9 cM) and two-point and multipoint linkage analysis were performed. In two-point linkage analysis, we identified two markers, D13S175 (6.03 cM) and D13S265 (68.73 cM) that had LOD scores greater than 1 for left ankle (LOD=2.09, LOD=1.49, respectively). We also found a marker D13S175 (6.03 cM) with a high LOD for left wrist (LOD=1.49) and the markers D13S265 (68.73 cM) and D13S217 (17.21 cM) for the right wrist (LOD= 1.82, LOD= 1.62, respectively). Among these significant marker regions, only two regions at 17 cM (13p11) and 65 cM (13q21) for the right wrist overlapped with major QTLs reported in following multipoint linkage analysis (LOD= 1.7549, LOD=1.4462, respectively). This study provides the possible evidence of the presence of QTLs affecting right wrist BMD in Mongolian populations on 13p11 and 13q21. Modest evidence was also found for genes affecting left ankle and left wrist BMD on 13p13.

• Journal of Ginseng Research
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• v.36 no.3
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• pp.298-307
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• 2012

Panax ginseng has been cultivated for centuries, and nine commercial cultivars have been registered in Korea. However, these nine elite cultivars are grown in less than 10% of ginseng fields, and there is no clear authentication system for each cultivar even though their values are higher than those of local landraces. Here, we have developed 19 microsatellite markers using expressed gene sequences and established an authentication system for all nine cultivars. Five cultivars, 'Chunpoong', 'Sunpoong', 'Gumpoong', 'Sunun', and 'Sunone', can each be identified by one cultivar-unique allele, gm47n-a, gm47n-c, gm104-a, gm184-a (or gm129-a), and gm175-c, respectively. 'Yunpoong' can be identified by the co-appearance of gm47n-b and gm129-c. 'Sunhyang' can be distinguished from the other eight cultivars by the co-appearance of gm47n-b, gm129-b, and gm175-a. The two other cultivars, 'Gopoong' and 'Cheongsun', can be identified by their specific combinations of five marker alleles. This marker set was successfully utilized to identify the cultivars among 70 ginseng individuals and to select true F1 hybrid plants between two cultivars. We further analyzed the homogeneity of each cultivar and phylogenetic relationships among cultivars using these markers. This marker system will be useful to the seed industry and for breeding of ginseng.

• Korean Journal of Plant Resources
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• v.30 no.3
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• pp.323-330
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• 2017

Eleutherococcus senticosus (Siberian ginseng) is an important medicinal tree found in northeast Asia. In this study, we analyzed the genome-wide distribution of microsatellites in E. senticosus. By sequencing 711 clones from an SSR-enriched genomic DNA library, we obtained 12 polymorphic SSR markers, which also revealed successful amplicons in E. senticosus accessions. Using the developed SSR markers, we estimated genetic diversity and population structure among 131 E. senticosus accessions in Korea and China. The number of alleles ranged from 2 to 11, with an average of 7.4 alleles. The mean values of observed heterozygosity ($H_O$) and expected heterozygosity ($H_E$) were 0.59 and 0.56, respectively. The average polymorphism information content (PIC) was 0.51 in all 131 E. senticosus accessions. E. senticosus accessions in Korea and China showed a close genetic similarity. Significantly low pairwise genetic divergence was observed between the two regions, suggesting a relatively narrow level of genetic basis among E. senticosus accessions. Our results not only provide molecular tools for genetic studies in E. senticosus but are also helpful for conservation and E. senticosus breeding programs.

• Journal of Gastric Cancer
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• v.8 no.4
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• pp.169-175
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• 2008

Purpose: The main target of 5-fluorouracil (5-FU) is thymidylate synthase (TS). A high TS expression has been identified as promoting resistance to 5-FU. For colorectal cancers, the response to 5-FU based adjuvant chemotherapy is different according to the microsatellite instability (MSI) status. The reports on the relationship between MSI and the TS expression in colorectal cancer have been inconsistent. No data is available for gastric cancer regarding the relationship between MSI and the TS expression. Therefore, we studied the relationship between MSI and the TS expression in gastric cancer. Materials and Methods: Ninety-nine consecutive patients who underwent radical gastrectomy for gastric cancer from January 2004 to May 2006 at Bundang CHA hospital were studied. MSI was assessed for five markers (BAT25, BAT26, D2S123, D5S346, and D17S250) by PCR and with using an ABI prism 3100 Genetic analyzer. The TS expression was analyzed by immunohistochemistry with using mouse anti-thymidylate synthase monoclonal antibody to the TS 106 clone. Results: Out of the ninety-nine patients, MSS/MSI-L was detected in 92 (92.1%) cases and 7 cases (7.1%) were MSI-H. A negative TS expression was found in 46 (46.5%) cases, a low TS expression was found in 33 (33.3%) and a high TS expression was found in 20 (20.2%). Out of 92 MSS/MSI-L patients, the number of patients with negative, low and high TS expressions were 46 (50%), 30 (32.6%) and 16 (17.4%), respectively. Out of the 7 MSI-H patients, the number of patients with negative, low and high TS expressions were 0 (0%), 3 (42.9%) and 4 (57.1%), respectively. The relationship between MSI-H and a high TS expression was statistically significant. Conclusion: Gastric cancer with MSI-H showed higher levels of a TS expression compared to the gastric cancer with MSS/MSI-L.