• Asian-Australasian Journal of Animal Sciences
• /
• v.25 no.8
• /
• pp.1063-1072
• /
• 2012

Effective population size ($N_e$) is an important measure to understand population structure and genetic variability in animal species. The objective of this study was to estimate $N_e$ in Sapsaree dogs using the information of rate of inbreeding and genomic data that were obtained from pedigree and the Illumina CanineSNP20 (20K) and CanineHD (170K) beadchips, respectively. Three SNP panels, i.e. Sap134 (20K), Sap60 (170K), and Sap183 (the combined panel from the 20K and 170K), were used to genotype 134, 60, and 183 animal samples, respectively. The $N_e$ estimates based on inbreeding rate ranged from 16 to 51 about five to 13 generations ago. With the use of SNP genotypes, two methods were applied for $N_e$ estimation, i.e. pair-wise $r^2$ values using a simple expectation of distance and $r^2$ values under a non-linear regression with respective distances assuming a finite population size. The average pair-wise $N_e$ estimates across generations using the pairs of SNPs that were located within 5 Mb in the Sap134, Sap60, and Sap183 panels, were 1,486, 1,025 and 1,293, respectively. Under the non-linear regression method, the average $N_e$ estimates were 1,601, 528, and 1,129 for the respective panels. Also, the point estimates of past $N_e$ at 5, 20, and 50 generations ago ranged between 64 to 75, 245 to 286, and 573 to 646, respectively, indicating a significant $N_e$ reduction in the last several generations. These results suggest a strong necessity for minimizing inbreeding through the application of genomic selection or other breeding strategies to increase $N_e$, so as to maintain genetic variation and to avoid future bottlenecks in the Sapsaree population.

• Asian Pacific Journal of Cancer Prevention
• /
• v.16 no.13
• /
• pp.5515-5519
• /
• 2015

The single nucleotide polymorphism (SNP) ss469415590 in the interferon lambda-4 (IFNL4) gene has recently been reported to have an association with treatment response in chronic hepatitis C. However, any importance of the SNP in association with response to pegylated interferon (PEG-IFN) therapy in patients with chronic hepatitis B (CHB) is unclear. We retrospectively analyzed data for Thai patients with CHB treated with PEG-IFN for 48 weeks. Virological response (VR) for HBeAg-positive CHB was defined as HBeAg seroconversion plus HBV DNA level <2,000 IU/mL at 24 weeks post-treatment. VR for HBeAg-negative CHB was defined as an HBV DNA level <2,000 IU/mL at 48 weeks. The SNP was identified by real time PCR using the TaqMan genotyping assay with MGB probes. A total 254 patients (107 HBeAg-positive and 147 HBeAg-negative) were enrolled in the study. The distribution of TT/TT, ${\Delta}G/TT$ and ${\Delta}G/{\Delta}G$ genotypes was 221 (87.0%), 32 (12.6%) and 1 (0.4%), respectively. Patients with non-TT/TT genotypes had significantly higher baseline HBV DNA levels than patients with the TT/TT genotype. In HBeAg-positive CHB, 41.2% of patients with TT/TT genotype versus 50.0% with non-TT/TT genotype achieved VR (P=0.593). In HBeAg-negative CHB, the corresponding figures were 40.3% and 43.5%, respectively (P=0.777). There was no significant correlation between the SNP genotypes and HBsAg clearance in both groups of patients. In summary, ss469415590 genotypes were not associated with response to PEG-IFN in Thai patients with HBeAg-positive and HBeAg-negative CHB.

• Journal of Mushroom
• /
• v.16 no.1
• /
• pp.51-56
• /
• 2018

In Korea, the oak mushroom (Lentinula edodes) is highly preferred by consumers in the food industry and makes up about 97.7% of the total forest mushroom production. This indicates that the oak mushroom is an important non-timber forest product in Korea. Recently, the breeding and development of new cultivars of L. edodes have been actively initiated, and the development of molecular markers that are able to identify and discriminate the new cultivars is crucial for protecting the breeder's rights. This study was carried out to develop a cleaved amplified polymorphic sequence (CAPS) marker for the identification and discrimination of a new cultivar, Sanmaru 2ho from the 37 other oak mushroom cultivars. A single nucleotide polymorphism (SNP) was identified at the $1,803,483^{rd}$ position of scaffold2 in the genome of Sanmaru 2ho. The amplified DNA containing the SNP of Sanmaru 2ho was uniquely not cleaved by the restriction enzyme, Hha I, and thus Sanmaru 2ho was successfully distinguished from the other oak mushroom cultivars.

• Asian-Australasian Journal of Animal Sciences
• /
• v.25 no.6
• /
• pp.794-799
• /
• 2012

The cytochrome P450c17-I (CYP17-I) is one of the enzymes critical to gonadal development and the synthesis of androgens. Two single nucleotide polymorphisms (SNPs) were detected within the coding region of the CYP17-I gene in a population of 75 male Japanese flounder (Paralichthys olivaceus). They were SNP1 (c.C445T) located in exon2 and SNP2 (c.T980C (p.Phe307Leu)) located in exon5. Four physiological indices, which were serum testosterone (T), serum $17{\beta}$-estradiol ($E_2$), Hepatosomatic index (HSI), and Gonadosomatic index (GSI), were studied to examine the effect of the two SNPs on the reproductive endocrines of Japanese flounder. Multiple comparisons revealed that CT genotype of SNP1 had a much lower T level than CC genotype (p<0.05) and the GSI of individuals with CC genotype of SNP2 was higher than those with TT genotype (p<0.05). Four diplotypes were constructed based on the two SNPs and the diplotype D3 had a significantly lower T level and GSI. In conclusion, the two SNPs were significantly associated with reproductive traits of Japanese flounder.

• Asian Pacific Journal of Cancer Prevention
• /
• v.14 no.5
• /
• pp.3051-3056
• /
• 2013

Background: Genetic aberrations of DNA repair enzymes are known to be common events associated with different cancer entities. The aim of the present study was to analyze genetic associations of rs1805404 (Asp81Asp) and rs1805414 (Ala284Ala) in the PARP1 gene with the risk of breast cancer in Saudi Arabia. Materials and Methods: These two SNP's were analyzed in a primary study group of breast cancer patients and healthy control subjects. Genotypes were determined by TaqMan SNP testing and analyzed using Chi-square or t test and logistic regression analysis with SPSS16.0 software. Results and Conclusions: Results showed that rs1805414 was associated with a significantly increased susceptibility to breast cancer, significant risk being observed for the TC, CC and TC+CC genotypes. In conclusion PARP1 rs1805414 SNP polymorphisms may be involved in the etiology of breast cancer in the Saudi population. In contrast, PARP1 rs1805404 did not show any significant association in overall in breast cancer samples when compared to healthy controls. Confirmation of our findings in larger populations of different ethnicities may provide evidence for a role of the PARP1 gene in breast carcinoma developnment.

• Asian-Australasian Journal of Animal Sciences
• /
• v.26 no.9
• /
• pp.1218-1228
• /
• 2013

Fat quality is determined by the composition of fatty acids. Genetic relationships between this composition and single nucleotide polymorphisms (SNPs) in the stearoyl-CoA desaturase1 (SCD1) gene were examined using 513 Korean native cattle. Single and epistatic effects of 7 SNP genetic variations were investigated, and the multifactor dimensionality reduction (MDR) method was used to investigate gene interactions in terms of oleic acid (C18:1), mono-unsaturated fatty acids (MUFAs) and marbling score (MS). The g.6850+77 A>G and g.14047 C>T SNP interactions were identified as the statistically optimal combination (C18:1, MUFAs and MS permutation p-values were 0.000, 0.000 and 0.001 respectively) of two-way gene interactions. The interaction effects of g.6850+77 A>G, g.10213 T>C and g.14047 C>T reflected the highest training-balanced accuracy (63.76%, 64.70% and 61.85% respectively) and was better than the individual effects for C18:1, MUFAs and MS. In addition, the superior genotype groups were AATTCC, AGTTCC, GGTCCC, AGTCCT, GGCCCT and AGCCTT. These results suggest that the selected SNP combination of the SCD1 gene and superior genotype groups can provide useful inferences for the improvement of the fatty acid composition in Korean native cattle.

• Korean Journal of Fisheries and Aquatic Sciences
• /
• v.36 no.2
• /
• pp.94-99
• /
• 2003

Mitochondrial DNAs has been used frequently as genetic markers for the population genetic studies of salmonid fishes. Samples used in this experiment were chum salmons (Oncorhynchus keta) from Korea. We analyzed variation of mitochondrial NADH dehydrogenase subunit 3 gene (ND3) among 4 individuals of the Korea population. Genomic DNA was extracted from the liver of the chum salmon samples. Then, the ND3 gene was amplified by polymerase chain reaction (PCR) including the 3' region of cytochrome oxidase III gene (COIII) and the 5` region of NADH dehydrogenase subunit 4L gene (ND4L). The size of the PCR product was 752 Up and the sequences showed some genetic variation among those four individuals. Genetic variations were observed in 7 sites as single nucleotide polymorphism (SNP). Within the open reading frame of the ND3 gene which encodes 116 amino acids, 5 nucleotide substitutions were found. Both transitional and transversional changes occurred more frequently with transitional changes. Comparison of these sequences with the others of a Japanese chum salmon in GenBank showed 5 sites of SNPs. This study provided the basic information of SNP in ND3 gene among Korean chum salmons and demonstrated the possible use of the SNP data as a genetic marker.

• Food Science of Animal Resources
• /
• v.30 no.6
• /
• pp.918-922
• /
• 2010

Due to the large amount of beef imported from the USA to Korea, Korean consumers have become increasingly interested in the country of origin since it can affect market prices. Previously, Bos indicus and Bos taurus-specific markers were developed for the purpose of cattle breed identification, specifically discrimination of Australian beef. In this study, six SNP markers derived from Illumina 50K bovine SNP chip data were used for the discrimination between Korean cattle (Hanwoo) and imported beef from USA. PCR-RFLP genotyping methods were also developed, which indicates that these markers can be applied relatively easily compared to other markers. Taking into account a discrimination rate of 55% based on MC1R marker between Hanwoo and imported beef from USA, two additional markers, SNPs 23803 and 34776, were ideal and resulted in probability of identification of 0.942 and probability of misjudgment of 0.03. Therefore, the markers developed in this study can greatly contribute to the correct discrimination between beef from USA and Hanwoo beef.

• Asian-Australasian Journal of Animal Sciences
• /
• v.31 no.8
• /
• pp.1078-1087
• /
• 2018

Objective: The genetic diversity of the Landrace population, a representative maternal pig breed in Korea, is important for genetic improvement. Previously, the effective population size (Ne) has been used to infer the genetic diversity of a population of interest. In this study, we aimed to use single nucleotide polymorphism (SNP) data to characterize linkage disequilibrium (LD) and the Ne of the Korean Landrace population. Methods: We genotyped 1,128 Landrace individuals from three representative Korean major grand-grand-parent (GGP) farms using the Illumina PorcineSNP60 version2 BeadChip, which covers >61,565 SNPs located across all autosomes and mitochondrial and sex chromosomes. We estimated the expected LD and current Ne, as well as ancestral Ne. Results: In the Korean Landrace population, the mean LD ($r^2$) of 3.698 million SNP pairs was $0.135{\pm}0.204$. The mean $r^2$ decreased slowly with as the distance between SNPs increased, and remained constant beyond 3 Mb. According to the $r^2$ calculations, 8,085 of 3.698 million SNP pairs were in complete LD. The current Ne (${\pm}$standard deviation) of the Korean Landrace population is approximately 92.27 [79.46; 105.07] individuals. The ancestral Ne exhibited a slow and steady decline from 186.61 to 92.27 over the past 100 generations. Additionally, we observed more a rapid Ne decrease from the past 20 to 10 generations ago, compared with other intervals. Conclusion: We have presented an overview of LD and the current and ancestral Ne values in the Korean Landrace population. The mean LD and current Ne for the Korean Landrace population confirm the genetic diversity and reflect the history of this pig population in Korea.

• Korean Journal of Agricultural Science
• /
• v.39 no.2
• /
• pp.219-226
• /
• 2012

The acyl-CoA dehydrogenase, C-2 to C-3 short chain (ACADS) gene is known to be related with fat metabolism, especially coverts the fat to the energy sources in cattle. In human, the mutations in this gene cause SCAD deficiency, which is one of the fatty acid metabolism disorders. The ACADS gene is located on bovine chromosome 17. The objective of this study was to identify SNPs in Hanwoo ACADS gene and identify the relationships with economic traits. In this study, two SNPs, T1570G SNP in exon 2 and G13917A SNP in exon 4, were observed. Moreover, in the coding region, 2 missense mutations, T (Cys) ${\rightarrow}$ G (Trp) mutation at 1570 bp and G (Arg) ${\rightarrow}$ A (Gln) mutation at 13917 bp, were observed. These mutations were subjected to the PCR-RFLP for typing 198 Hanwoo animals. The observed genotype frequency for T1570G was 0.135 (TT), 0.860 (TG) and 0.005 (GG), respectively. Also, 0.900 (GG) and 0.100 (GA) were observed for the G13917A mutation. The association of these SNPs with four economic traits, CW (Carcass Weight), BF (Backfat Thickness), LMA (Longissimus Muscle Area), MS (Marbling Score), were also observed. The results indicated that no significant results were observed in all four traits (P>0.05). This might indicate that further studies are ultimately needed to use the SNPs in ACADS gene in lager populations for effectively used for the marker assisted selection.