• Journal of Animal Science and Technology
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• v.57 no.12
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• pp.47.1-47.10
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• 2015

Background: Knowledge of linkage disequilibrium (LD) levels among different populations can be used to detect genetic diversity and to investigate the historical changes in population sizes. Availability of large numbers of SNP through new sequencing technologies has provided opportunities for extensive researches in quantifying LD patterns in cattle breeds. The aim of this study was to compare the extent of linkage disequilibrium among Iranian cattle breeds using high density SNP genotyping data. Results: A total of 70 samples, representing seven Iranian indigenous cattle breeds, were genotyped for 777962 SNPs. The average values of LD based on the $r^2$ criterion were computed by grouping all syntenic SNP pairwises for intermarker distances from 0 Kb up to 1 Mb using three distance sets. Average $r^2$ above 0.3 was observed at distances less than 30 Kb for Sistani and Kermani, 20 Kb for Najdi, Taleshi, Kurdi and Sarabi, and 10 Kb for Mazandarani. The LD levels were considerably different among the Iranian cattle breeds and the difference in LD extent was more detectable between the studied breeds at longer distances. Lower level of LD was observed for Mazandarani breed as compared to other breeds indicating larger ancestral population size in this breed. Kermani breed continued to have more slowly LD decay than all of the other breeds after 3 Kb distances. More slowly LD decay was observed in Kurdi and Sarabi breeds at larger distances (>100 Kb) showing that population decline has been more intense in more recent generations for these populations. Conclusions: A wide genetic diversity and different historical background were well reflected in the LD levels among Iranian cattle breeds. More LD fluctuation was observed in the shorter distances (less than 10 Kb) in different cattle populations. Despite of the sample size effects, High LD levels found in this study were in accordance with the presence of inbreeding and population decline in Iranian cattle breeds.

• Biomedical Science Letters
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• v.18 no.4
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• pp.377-383
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• 2012

Recent genome-wide association studies (GWAS) have identified a number of common variants associated with blood pressure homeostasis and hypertension in population. In the previous study, single nucleotide polymorphisms (SNPs) in the SLC4A4 gene have been reported to be associated with hypertension in Han Chinese population. We aimed to confirm whether the genetic variation of SLC4A4 gene influence the susceptibility to blood pressure and hypertension in Korean population. We genotyped variants in or near SLC4A4 in a population-based cohort including 7,551 unrelated Korean from Ansan and Ansung. Here, we performed association analysis to elucidate the possible relations of genetic polymorphisms in SLC4A4 gene with blood pressure traits. By examining genotype data of a total of 7,551 subjects in the Korean Association REsource (KARE) study, we discovered the SLC4A4 gene polymorphisms are associated with blood pressure and hypertension. The common and highest significant polymorphism was rs6846301 (${\beta}$=0.839, additive P=0.032) with systolic blood pressure (SBP), rs6846301 (${\beta}$=0.588, additive P=0.027) with diastolic blood pressure (DBP), and rs6846301 (OR=1.23, CI: 1.09~1.40, additive $P=1.2{\times}10^{-3}$) with hypertension. Furthermore, the SNP rs6846301 was consistently associated with both blood pressure and hypertension. Consequently, we found statistically significant SNPs in SLC4A4 gene that are associated with both blood pressure and hypertension traits. In addition, these results suggest that the individuals with the minor alleles of the SNP in the SLC4A4 gene may be more susceptible to the development of hypertension in the Korean population.

• Korean Journal of Plant Resources
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• v.28 no.3
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• pp.341-349
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• 2015

Magnoliae Flos (Sini in Korean) is one of the most important oriental medicinal plants. In the Korean Herbal Pharmacopeia, the bud of the all species in Manolia denudate and Manolia genus were regarded as the botanical sources for ‘Sini’. Most the dried bud of Manolia denudata, Manolia biondii and Manolia sprengeri were used as ‘Xin-yi’ in China. Therefore, the purpose of this study was to determine and compare the ‘Magnolia’ species, four species including Manolia denudata, M. biondii, M. liliiflora and M. Kobus were analysis of sequencing data revealed DNA polymorphisms. The based on tRNA coding leucine/phenylalanine (trnL-F) and NADH-plastoquinone oxidoreductase subunit 5 (ndhF) sequences in chloroplast DNA. For the identification of ‘Magnolia’ species, polymerase chain reaction (PCR) analysis of chloroplast DNA regions such as ndhF have proven an appropriate method. A single nucleotide polymorphism (SNP) has been identified between genuine “Sini” and their fraudulent and misuse. Specific PCR primers were designed from this polymorphic site within the sequence data, and were used to detect true plants via multiplex PCR.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.3
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• pp.1051-1056
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• 2015

Aberrant expression of genes in de novo lipogenesis (DNL) pathway were associated with various cancers, including hepatocellular carcinoma (HCC). Single nucleotide polymorphisms (SNPs) of DNL genes have been reported to be associated with prognosis of some malignancies. However, the effects of SNPs in DNL genes on overall survival of HCC patients receiving transarterial chemoembolization (TACE) treatment are still unknown. In present study, nine SNPs in three genes (ACLY, ACACA and FASN) in DNL pathway were genotyped using the Sequenom iPLEX genotyping system in a hospital-based cohort with 419 HCC patients treated with TACE, and their associations with HCC overall survival were evaluated by Cox proportional hazard regression analysis under three genetic models (additive, dominant and recessive). Although we did not find any significant results in total analysis (all p>0.05), our stratified data showed that SNP rs9912300 in ACLY gene was significantly associated with overall survival of HCC patients with lower AFP level and SNP rs11871275 in ACACA gene was significantly associated with overall survival of HCC patients with higher AFP level. We further identified the significant interactions between AFP level and SNP rs9912300 or rs11871275 in the joint analysis. Conclusively, our data suggest that genetic variations in genes of DNL pathway may be a potential biomarker for predicting clinical outcome of HCC patients treated with TACE.

• Journal of Life Science
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• v.20 no.3
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• pp.462-465
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• 2010

Sweetness plays an important role in providing calories and promoting appetite for food. Since it has been known that genetic factor(s) is involved in individual differences in taste sensitivity in humans, this study aimed to examine genetic variations of the TAS1R2 gene, one of the components for tasting sweet compounds, by using DNA sequencing analysis from 98 unrelated Korean subjects. As a result, 12 different single nucleotide polymorphisms (SNPs) were identified in the hTAS1R2 gene and most of them were nonsynonymous. Also, two novel SNPs were found for the first time in this study. It was noted that the frequencies of these SNPs were common in the Korean population. 20 different haplotypes with coding SNPs (cSNPs) were also found in this study. Three out of these haplotypes were common, showing frequencies of > 10%. The repertoire and frequencies of cSNPs and haplotypes in the hTAS1R2 gene will provide information that will help identify a functional ligand receptor common in the Korean population.

• Animal Bioscience
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• v.36 no.1
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• pp.10-18
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• 2023

Objective: In this study, we aimed to position the Hungarian Merino among other Merinoderived sheep breeds, explore the characteristics of our sampled animals' genetic similarity network within the breed, and highlight single nucleotide polymorphisms (SNPs) associated with daily weight-gain. Methods: Hungarian Merino (n = 138) was genotyped on Ovine SNP50 Bead Chip (Illumina, San Diego, CA, USA) and positioned among 30 Merino and Merino-derived breeds (n = 555). Population characteristics were obtained via PLINK, SVS, Admixture, and Treemix software, within-breed network was analysed with python networkx 2.3 library. Daily weight gain of Hungarian Merino was standardised to 60 days and was collected from the database of the Association of Hungarian Sheep and Goat Breeders. For the identification of loci associated with daily weight gain, a multi-locus mixed-model was used. Results: Supporting the breed's written history, the closest breeds to Hungarian Merino were Estremadura and Rambouillet (pairwise F_ST values are 0.035 and 0.036, respectively). Among Hungarian Merino, a highly centralised connectedness has been revealed by network analysis of pairwise values of identity-by-state, where the animal in the central node had a betweenness centrality value equal to 0.936. Probing of daily weight gain against the SNP data of Hungarian Merinos revealed five associated loci. Two of them, OAR8_17854216.1 and s42441.1 on chromosome 8 and 9 (-log₁₀P>22, false discovery rate<5.5e-20) and one locus on chromosome 20, s28948.1 (-log₁₀P = 13.46, false discovery rate = 4.1e-11), were close to the markers reported in other breeds concerning daily weight gain, six-month weight, and post-weaning gain. Conclusion: The position of Hungarian Merino among other Merino breeds has been determined. We have described the similarity network of the individuals to be applied in breeding practices and highlighted several markers useful for elevating the daily weight gain of Hungarian Merino.

• KIPS Transactions on Software and Data Engineering
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• v.2 no.10
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• pp.697-704
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• 2013

The identification of haplotypes, which encode SNPs in a single chromosome, makes it possible to perform haplotype-based association tests with diseases. Minimum Error Correction model, one of models to computationally assemble a pair of haplotypes for a given organism from Single Nucleotide Polymorphism fragments, has been known to be NP-hard even for gapless cases. In the previous work, an improved branch and bound algorithm was suggested and showed that it is more efficient than naive branch and bound algorithm by performing experiments for Apis mellifera (honeybee) data set. In this paper, to show the extensibility of the algorithm to other organisms we apply the improved branch and bound algorithm to the human data set and confirm the efficiency of the algorithm.

• Korean Journal of Poultry Science
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• v.41 no.3
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• pp.191-196
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• 2014

The identification and utilization of potential candidate genes with significant effects on economically important traits have become increasingly important in poultry breeding programs. The ovocalyxin-32 (OCX-32) gene is located chromosome 9 in chicken, plays an important role in eggshell formation. This study was performed to assess the association between single nucleotide polymorphisms (SNPs) of OCX-32 gene and egg production traits in the Korean native chicken. Four Korean native chicken population (n = 181; including 46 females of Ogol, 46 females of white, 43 females of gray and 46 females of black) were used to analyze two SNPs (c.494A>C and c.267T>G) in the OCX-32 gene by PCR-RFLP (Polymerase Chain Reaction-Restricted Fragment Length Polymorphism). We measured egg production traits of age at first egg, first egg weight, egg production ratio and egg weight. The SNP c.494A>C was significantly associated with egg production ratio in Korean Ogol chickens (p<0.001) and egg weight in Korean white chickens (p<0.05). SNP c.267T>C was significantly associated with egg weight in Korean Ogol chickens (p<0.05). But there was no significant association in Korean gray and black chickens. Results suggest the possibility of using molecular markers in OCX-32 gene as a tool for performance and egg production traits in Korean native chicken breeding program.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.11
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• pp.1755-1762
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• 2020

Objective: Thyroid hormone responsive spot 14 alpha (THRSP) has been used to investigate the regulation of de novo lipogenesis because the variation of THRSP mRNA content in the tissue affects directly the ability of that tissue to synthetize lipids. Also, this gene responds to thyroid hormone stimulation and high level of carbohydrate feeding or insulin-injection. This study was carried out to investigate variations within THRSP and their effects on body and carcass weights in Korean native chicken (KNC). Methods: A total of 585 chickens which represent the five lines of KNC (Black, Gray-Brown, Red-Brown, White, and Yellow-Brown) were reared and body weight data were recorded every two weeks from hatch until 20 weeks of age. Polymerase chain reaction- restriction fragment length polymorphism, DNA chips for Agilent 2100 Bioanalyzer, and Fluidigm Genotyping Technology, were applied to genotype selected markers. A linear mixed-effect model was used to access association between these single nucleotide polymorphism (SNP) markers and growth-related traits. Results: A total of 30 polymorphisms were investigated in THRSP. Of these, nine SNPs for loci were selected to perform association analyses. Significant associations were detected between g.-49G>T SNP with body weight at 20 weeks of age (BW20), g.451T>C SNP with growth at 10 to 12 weeks of age (GR10-12), and g.1432A>C SNP with growth at 14 to 16 weeks trait (GR14-16) and body weight at 18 weeks of age (BW18). Moreover, diplotype of the THRSP gene significantly affected body weight at 12 weeks of age (BW12) and GR10-12 traits. Diplotype of ht1/ht2 was favorable for BW12 and GR10-12 traits. Conclusion: These results suggest that THRSP can be regarded as a candidate gene for growth traits in KNC.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.19 no.9
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• pp.116-123
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• 2018

The sperm quality is determined by the kinetic characteristics and acrosome integrity of the sperm. In the previous studies, analysis of semen quality had large errors because those experiments by using microscope had been conducted by people. In recent years, the molecular biological methods have been newly developed to complement the previous techniques. The ZAR1 gene is known to be a gene that affects early embryonic development in vertebrates, but there is no study of the association with semen. In this study, we analyzed the association between the kinetic characteristics and ZAR1 single nucleotide polymorphism (SNP) genotype. To detect the SNPs, we performed sequencing using genomic DNA from the whole bloods of Duroc pigs. We identified an SNP in the ZAR1 gene g.2540T>C. ZAR1 SNP genotypeing in 105 pigs revealed that the major and minor alleles were T and C, respectively. After we analyzed the association between the kinetic characteristics of sperm and the ZAR1 SNP genotype, we found a significant association in MOT (p<0.01), VSL (p<0.05) of the kinetic characteristics in the Duroc boars. It was confirmed that the boars with T allele were lower in MOT and VSL than C allele. Therefore, pigs with C allele are judged to be better at the MOT and VSL of semen. Based on these results, ZAR1 SNP genotyping may be a useful molecular biomarker to improve semen quality by applying molecular breeding technology.