• Journal of the Korean Data and Information Science Society
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• v.18 no.3
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• pp.599-608
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• 2007

This study was conducted to establish an individual identification system in Hanwoo cattle. Samples of 33 Hanwoo individuals from Korean elite sire families were used. Thirteen major microsatellite markers were selected from alleles amplified, their frequencies, H(Heterozygosity) and PIC(Polymorphism Information Content) with Hardy-Weinberg equilibrium. Next, in order to evaluate the power of the markers selected on the individual animal identification, MP(Match probability) and R(Relatedness coefficient) with the percentage of animal incorrectly identified were computed. Finally nine microsatellite markers were selected and discussed.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.22-22
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• 2017

Genetic diversity is one of fundamental parameters for rice cultivar improvement. Rice mutants are also a new source for rice breeding innovation. In this study, ninety-three SSR markers were applied to evaluate the genetic variation among nineteen rice mutant lines. The results showed that a total of 169 alleles from 56 polymorphism markers was recorded with an average of 3.02 alleles per locus. The values of polymorphism information content (PIC) varied from 0.09 to 0.79. The maximum number of alleles was 7, whereas the minimum number of alleles was 2. The heterozygosity values ranged from 0.10 to 0.81. Four clusters were generated using the unweighted pair group method with arithmetic mean (UPGMA) clustering. Fourteen phenotype characteristics were also evaluated. The correlation coefficient values among these phenotye characteristics were obtained in this study. Genetic diversity information of rice mutant lines can support rice breeders in releasing new rice varieties with elite characterisitics.

• 한국생물공학회:학술대회논문집
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• 2000.04a
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• pp.592-595
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• 2000

In human chromosome, a short sequence of DNA has been repeated a number of times. These repeats are called variable number of tandem repeat(VNTR) or short tandem repeat(STR) which has short repeat core. VNTR and STR are used in the field of forensic science, evolution, and anthropology. In this work, we examined allele frequencies of 3 VNTR(YNZ22, NeuR, D21S11) and one STR(Humth01) in a Korean population sample by polymerase chain reaction(PCR) followed by high-resolution polyacrylamide gelelectrophoresis(PAGE) with silver staining. Subsequently, the polymorphism information content(PIC) was calculated : the highest PIC was observed for the NeuR locus(0.95680) and lowest for the Humth01 locus(0.75809).

• Biotechnology and Bioprocess Engineering:BBE
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• v.5 no.3
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• pp.169-173
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• 2000

On human chromoscomes, a short sequence of DNA is known to repeat a number of times. These are called variable number of tandem repeat (VNTR) or short tandem respeat (STR) which has a short core. VNTR and STR are used in the filed of forensic science, evolution, and anthropology. In this work, we examined allele frequencies of one VNTR (YNZ22) and three STRs (NeuR, D21S11, Humth01) in a korean population sample by polymerase chain reaction (RCP) followed by high-resolution polyacrylamide gel electro-phoresis (PAGE) with silver stain. Subsequently, the polymorphism information content (PIC) was calculated : the hifhest PIC was observed in the NeuR locus (0.95680) and lowest in the Humth01 locus (0.75809).

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.7
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• pp.938-943
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• 2002

This study was perfonned to detect polymorphisms of the two candidate genes, bovine BTN (Butyrophilin) and ST AT5a (Signal Transducers and Activators of Transcription) gene using 98 Holstein bulls' frozen semen, and to offer the basic information for QTL (Quantitative Trait Loci) analysis. Each BTN PCR product was digested with endonuclease restriction enzyme. The digested fragments of four BTN PCR products were observed as follows: 316,280, and 162 bp in BTN1, 568, 305 and 263 bp in BTN2, 576, 332, and 244 bp in BTN3, and 573, 291, and 282 bp in BTN4, respectively. The gene frequencies of A and B allele in four BTN loci were as follows: 0.8980 and 0.1020 in BTN1, 0.5510 and 0.4490 in BTN2, 0.8163 and 0.1837 in BTN3, and 0.8875 and 0.1122 in BTN4, respectively. And three genotypes (homotypel, heterotype, and homotype2) for STAT5a were observed by SSCP (single stranded conformational polymorphism) method and the genotype frequencies are 78.57%, 19.39%, and 2.04%, respectively. The PlC (Polymorphism Information Content) value and heterozygosity of four BTN loci were as follows: 0.1695 and 0.1870 in BTN1, 0.3713 and 0.4927 in BTN2, 0.2549 and 0.2999 in BTN3, and 0.1794 and 0.1992 in BTN4, respectively. Comparing with the reported data, PlC value of BTN2 might have the possibility to be useful marker. Other BTN loci indicated skewed allele distribution.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.6
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• pp.784-788
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• 2006

Microsatellite polymorphism and the genetic relationship were estimated using genotype information of 305 horses from 11 microsatellite loci. The breeds include the indigenous Korean breeds, Korean native horse (102) and Jeju racing horse (56) together with Japan Hokkaido horse (5), Mongolian horse (19), Thoroughbred horse (108), Quarter horse (11) and Przewalskii horse (4). Allelic frequencies, the number of alleles per locus were estimated by direct counting from observed genotype, and genetic variability was computed using the CERVUX software and DISPAN. The number of alleles per locus varied from 6 (HMS6) to 18 (ASB17) with an average value of 10.45 in horse breeds. The expected total heterozygosity ($H_T$) and coefficient of gene differentiation ($G_{ST}$) ranged 0.764-0.921 (the average value was 0.830) and 0.102-0.266 (the average value was 0.180) in horse breeds, respectively. Four populations (Przewalskii horse, Japan Hokkaido horse, Quarter horse, Thoroughbred horse) showed lower heterozygosity than the average value (the average value was 0.710). The expected heterozygosity within breed ($H_S$) and mean no. of observed alleles ranged from $0.636{\pm}0.064$ (Japan Hokkaido horse) to $0.809{\pm}0.019$ (Mongolian horse), and from 2.73 (Przewalskii horse) to 8.27 (Korean native horse), respectively. The polymorphic information content (PIC) ranged from 0.490 (Przewalskii horse) to 0.761 (Mongolian horse) with an average value of 0.637 in horse breeds. The results showed three distinct clusters with high bootstrap support: the Korean native horse cluster (Korean native horse, Mongolian horse), the European cluster (Przewalskii horse, Thoroughbred horse), and other horse cluster (Jeju racing horse, Japan Hokkaido horse, and Quarter horse). A relatively high bootstrap value was observed for the Korean native horse cluster and European cluster (87%), and the Korean native horse and Mongolian horse (82%). Microsatellite polymorphism data were shown to be useful for estimating the genetic relationship between Korean native horse and other horse breeds, and also be applied for parentage testing in those horse breeds.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.6
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• pp.752-756
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• 2011

Polymorphism of the second exon of the caprine leukocyte antigen-DRB3 gene (CLA-$DRB3^*02$) was investigated in this study. The 285 bp PCR product of 258 individuals from 10 domestic goat breeds in Southwest China was digested with restriction endonucleases PstI and HaeIII and then genotyped. Three alleles and 4 restriction digestion profiles were distinguished by digestion of the PCR fragment by PstI, and 8 alleles and 13 genotypes by HaeIII. For HaeIII restriction enzyme sites, the Chi-square ($X^2$) test showed that all goat breeds in this study did not fit with the Hardy-Weinberg equilibrium (p<0.01 or p<0.05). The highly polymorphic nature of CLA-$DRB3^*02$ was demonstrated and the ranges of gene heterozygosity (He) and polymorphism information content (PIC) were 0.36-0.63 and 0.32-0.55, respectively. Clustering analysis showed that the 10 goat breeds clustered into two groups and Dazu Black goat had a close genetic relationship with Chengdu Grey, Jintang Black and Nanjiang Yellow goats.

• Journal of Forest and Environmental Science
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• v.29 no.3
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• pp.200-210
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• 2013

Biochemical characteristics of 24 Pongamia pinnata genotypes (candidate plus trees) from three agroclimatic zones were estimated and molecular characterization through RAPD markers was done. Various biochemical characters viz. seed oil, total carbohydrates, protein, acid value and Iodine number recorded significant variation among different genotypes. The highest seed oil content was 41.87% while seeds of 14 genotypes recorded above average (32.11%) for the trait. Seed oil and protein content exhibited a significant positive correlation and moderate heritability. Out of the initially selected twenty-five random primers, twenty-two RAPD primers were found to be highly reproducible and produced a total of 183 loci of which 147 (80.32%) loci were polymorphic. Percentage of polymorphism varied from 44% to 100% with an average of 80.62%. High level of genetic variation was found among different genotypes of P. pinnata. Both molecular and oil content (biochemical) markers appeared useful in analyzing the extent of genetic diversity in Pongamia and the result of these analyses will help to better understand the genetic diversity and relationship among populations. Overall, the Pongamia genotypes included in the study showed a correlation with their geographical origins such that genotypes from the same region tend to have higher genetic similarity as compared to those from different regions. However, in UPGMA based Nei's analysis, some genotypes were found not to be grouped based on geographical origins possibly due to the exchange of germplasm over time between farmers across the regions. The results from oil content analyses showed that several genotypes in 'Central and Western Plateau' agroclimatic zone of Jharkhand displayed a good potential for high oil content. The study provides insight about P. pinnata populations in Jharkhand (India) and constitutes a set of useful background information that can be used as a basis for future breeding strategy and improvement of the species.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.1
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• pp.58-62
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• 2019

Objective: The oxidized low density lipoprotein receptor 1 (OLR1) gene plays an important role in the degradation of oxidized low-density lipoprotein and adipocyte proliferation in mammals. For this reason, we aimed at investigating the association of OLR1 gene polymorphisms with carcass quality traits in Chinese Qinchuan cattle. Methods: The single nucleotide polymorphism (SNP) was identified in the 3' untranslated region of bovine OLR1 gene by DNA sequencing. In addition, the haplotype frequency and linkage disequilibrium estimates of three SNPs were evaluated in 520 individuals. Results: Results indicated that the studied three SNPs were within the range of moderate genetic diversity (0.25< polymorphism information content<0.5). Haplotype analysis of three SNPs showed that ten different haplotypes were identified, but only five haplotypes were listed as those with a frequency of <0.05 were excluded. The Hap3 ($-G_1T_2C_3-$) had the highest haplotype frequency (42.10%). Linkage disequilibrium analysis showed that the three SNPs had a low linkage ($r^2<0.001$). The T10588C and C10647T were significantly associated with backfat thickness and intramuscular fat content in Qinchuan cattle. Conclusion: Based on our results, we believe that the OLR1 gene could be a strong candidate gene for influencing carcass quality traits in Qinchuan cattle.

• Korean Journal of Breeding Science
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• v.42 no.1
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• pp.28-34
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• 2010

Diversity of 30 Korean potato cultivars was evaluated using 14 microsatellite markers. Twelve microsatellite markers representing 12 loci in the potato genome detected 84 polymorphisms among 30 cultivars and revealed alleles with a mean of 7.00 alleles per primer. The polymorphism information content (PIC) value ranged from 0.57 to 0.93 with average of 0.82. Based on polymorphism, cluster analysis was conducted by the unweighted pair-group method with arithmetic average (UPGMA) methods. Thirty potato varieties were distinctly separated into 2 groups and similarity coefficient of cluster ranged from 0.58 to 0.95. Thirty tetraploid cultivars were evaluated for six important agronomic traits. One-way analysis of variance was done to look for the degree of relationships between individual markers and traits. K1 and K2 markers showed a significant association with amylose contents, starch contents, and specific gravity.