• Genomics & Informatics
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• v.14 no.4
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• pp.181-186
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• 2016

Glucose tolerance tests have been devised to determine the speed of blood glucose clearance. Diabetes is often tested with the standard oral glucose tolerance test (OGTT), along with fasting glucose level. However, no single test may be sufficient for the diagnosis, and the World Health Organization (WHO)/International Diabetes Federation (IDF) has suggested composite criteria. Accordingly, a single multi-class trait was constructed with three of the fasting phenotypes and 1- and 2-hour OGTT phenotypes from the Korean Association Resource (KARE) project, and the genetic association was investigated. All of the 18 possible combinations made out of the 3 sets of classification for the individual phenotypes were taken into our analysis. These were possible due to a method that was recently developed by us for estimating genomic associations using a generalized index of dissimilarity. Eight single-nucleotide polymorphisms (SNPs) that were found to have the strongest main effect are reported with the corresponding genes. Four of them conform to previous reports, located in the CDKAL1 gene, while the other 4 SNPs are new findings. Two-order interacting SNP pairs of are also presented. One pair (rs2328549 and rs6486740) has a prominent association, where the two single-nucleotide polymorphism locations are CDKAL1 and GLT1D1. The latter has not been found to have a strong main effect. New findings may result from the proper construction and analysis of a composite trait.

• The korean journal of orthodontics
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• v.34 no.3 s.104
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• pp.261-267
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• 2004

Nonsyndromic cleft lip and/or palate (NSCLP) is one of the most common congenital deformities and its prevalence in Far East Asia, such as within Korean and Japanese populations, is relatively high. However, in the eastern part of Europe, clefts are relatively rare situations. These ethnic differences infer a genetic background of the disease. The objective of this study was to compare the frequency of single nucleotide polymorphism (SNP) in $TGF-{\beta}3$ between Korean and Romanian cleft families. Korean cleft families samples were collected from twenty-six families (n=78) and Romanian cleft families samples were collected from eighteen families (n=41). For sequencing, the blood or saliva of the subjects was sampled. A single nucleotide polymorphism was observed in the intron 5 of $TGF-{\beta}3$ (Al8141G). The frequency of each allele was significantly different between the Korean and Romanian samples. The Ah allele was present in 18 out of 78 Korean samples (23.1%) and in 27 out of 41 Romanian samples (65.9%). The AG was present in 27 (34.6%) out of 78 Koreans and in 13 (31.7%) out of 41 Romanians. The GG was found in 33 (42.3%) Koreans and in 1 (2.4%) Romanian. The difference between the groups was significant (p<0.001). In conclusion, the frequency of observed SNP was significantly different between the two countries. SNP in $TGF-{\beta}3$ in the Korean population seemed to have a higher possibility of occurrence for nonsyndromic cleft palate than the Romanian population.

• The Journal of the Korea Contents Association
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• v.16 no.10
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• pp.435-442
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• 2016

Obesity extends the global economic burden and it causes that the failure of a reduction of physical activity, and diet management. In this work, nutritional information and personalized diet based on calorie supply system and is discriminatory utilized the obesity-related SNP information in order to recommend a personalized functional foods. This study performed a GWAS analysis for the excavation of a Korean-specific and obesity-related SNP, which utilizes genetic information were recommended by entering a personalized diet in accordance with the SNP genotype-phenotype information. In addition, we integrated Database with relation of nutrient for utilizing the USDA Food information and it was applied to recommend with Sickdanome. As a result, the obesity-related SNP information was confirmed in the sample which has the normal value BMI. In this study, we have recognized that the phenotype information related obesity, BMI is inconsistent with the SNP genotype information. This result is shown that it is necessary to provide the personalized dietary SickdanOme recommendation based on the both pheotype-genotype information.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.7
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• pp.917-922
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• 2008

A disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif (ADAMTS1) plays a critical role in follicular rupture and represents a major advance in the proteolytic events that control ovulation. In this study, a 9,026-bp DNA sequence containing the full coding region, all 8 introns and part of the 5'and 3' untranslated region of the porcine ADAMTS1 gene was obtained. Analysis of the ADAMTS1 gene using the porcine radiation hybrid panel indicated that pig ADAMTS1 is closely linkage with microsatellite marker S0215, located on SSC13q49. The open reading frame of its cDNA covered 2,844 bp and encoded 947 amino acids. The coding region of porcine ADAMTS1 as determined by sequence alignments shared 85% and 81% identity with human and mouse cDNAs, respectively. The deduced protein contained 947 amino acids showing 85% sequence similarity both to the human and mouse proteins, respectively. Comparative sequencing of three pig breeds revealed one single nucleotide polymorphism (SNP) within exon 7 of which a G-C substitution at position 6006 changes a codon for arginine into a codon for proline. The substitution was situated within a PvuII recognition site and developed as a PCR-RFLP marker for further use in population variation investigations and association analysis with litter size. Allele frequencies of this SNP were investigated in seven pig breeds/lines. An association analysis in a new Qingping female line suggested that different ADAMTS1 genotypes have significant differences in litter size (p<0.01).

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.8
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• pp.1073-1082
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• 2012

We first sought to clarify the effects of discounted rate, survival rate, and lactation persistency as a component trait of the selection index on net merit, defined as the first five lactation milks and herd life (HL) weighted by 1 and 0.389 (currently used in Japan), respectively, in units of genetic standard deviation. Survival rate increased the relative economic importance of later lactation traits and the first five lactation milk yields during the first 120 months from the start of the breeding scheme. In contrast, reliabilities of the estimated breeding value (EBV) in later lactation traits are lower than those of earlier lactation traits. We then sought to clarify the effects of applying single nucleotide polymorphism (SNP) on net merit to improve the reliability of EBV of later lactation traits to maximize their increased economic importance due to increase in survival rate. Net merit, selection accuracy, and HL increased by adding lactation persistency to the selection index whose component traits were only milk yields. Lactation persistency of the second and (especially) third parities contributed to increasing HL while maintaining the first five lactation milk yields compared with the selection index whose only component traits were milk yields. A selection index comprising the first three lactation milk yields and persistency accounted for 99.4% of net merit derived from a selection index whose components were identical to those for net merit. We consider that the selection index comprising the first three lactation milk yields and persistency is a practical method for increasing lifetime milk yield in the absence of data regarding HL. Applying SNP to the second- and third-lactation traits and HL increased net merit and HL by maximizing the increased economic importance of later lactation traits, reducing the effect of first-lactation milk yield on HL (genetic correlation ($r_G$) = -0.006), and by augmenting the effects of the second- and third-lactation milk yields on HL ($r_G$ = 0.118 and 0.257, respectively).

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.12
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• pp.1809-1815
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• 2019

Objective: Copy number variations (CNVs) are a major source of genetic diversity complementary to single nucleotide polymorphism (SNP) in animals. The aim of the study was to perform a comprehensive genomic analysis of CNVs based on high density whole-genome SNP markers in Chinese Dongxiang spotted pigs. Methods: We used customized Affymetrix Axiom Pig1.4M array plates containing 1.4 million SNPs and the PennCNV algorithm to identify porcine CNVs on autosomes in Chinese Dongxiang spotted pigs. Then, the next generation sequence data was used to confirm the detected CNVs. Next, functional analysis was performed for gene contents in copy number variation regions (CNVRs). In addition, we compared the identified CNVRs with those reported ones and quantitative trait loci (QTL) in the pig QTL database. Results: We identified 871 putative CNVs belonging to 2,221 CNVRs on 17 autosomes. We further discarded CNVRs that were detected only in one individual, leaving us 166 CNVRs in total. The 166 CNVRs ranged from 2.89 kb to 617.53 kb with a mean value of 93.65 kb and a genome coverage of 15.55 Mb, corresponding to 0.58% of the pig genome. A total of 119 (71.69%) of the identified CNVRs were confirmed by next generation sequence data. Moreover, functional annotation showed that these CNVRs are involved in a variety of molecular functions. More than half (56.63%) of the CNVRs (n = 94) have been reported in previous studies, while 72 CNVRs are reported for the first time. In addition, 162 (97.59%) CNVRs were found to overlap with 2,765 previously reported QTLs affecting 378 phenotypic traits. Conclusion: The findings improve the catalog of pig CNVs and provide insights and novel molecular markers for further genetic analyses of Chinese indigenous pigs.

• Journal of Animal Science and Technology
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• v.54 no.5
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• pp.375-379
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• 2012

This study was carried out to define the "Wolla" coat color using 376 Jeju registered horses (white patched 142, solid coat color 234). Three major factors related to the white patches i.e ECA3-inversion for Tobiano, EDNRB 2 bp nucleotide substitution for frame Overo, and the KIT intron 16 single nucleotide polymorphism (SNP) for Sabino types of coat color were analyzed. It was found that out of 142 Jeju horses with white patches that have the genotype for ECA3-inversion (To) 140 horses were +/To heterozygous and 2 horses were To/To homozygous all Jeju horses with white patches had ECA3-inversion allele. However, there was no frame Overo or Sabino allele type in EDNRB and KIT intron 16 SNP in Jeju horses with white patches. As for 234 Jeju horses with a solid coat color, there was no ECA3-inversion allele related to the white patches. Thus, it could be considered that Wolla coat color with white patches in Jeju horses might have come from the Tobiano line in the genetic classification by coat color.

• Journal of Life Science
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• v.21 no.1
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• pp.155-158
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• 2011

Uncoupling protein (UCP) 3 has a number of proposed roles in the regulation of fatty acid metabolism. A number of polymorphisms in the human UCP3 gene have been identified, and the correlation with obesity related phenotypes evaluated. The objective of this study was to identify SNP in porcine UCP3 gene and to investigate the effect of the SNP on economic traits. The sequencing analysis method was used to identify nucleotide polymorphisms at position 1405 bp (Genebank accession No : AY739704) in porcine UCP3 gene. The SNP (G150R), located in the exon 3, changed the amino acid to glycine (GGG) from arginine (AGG). This G150R showed three genotypes - GG, GR and RR - by digestion with the restriction enzyme Sma Ⅰ using the PCR-RFLP method. The G150R showed significant effects only on back fat (P<0.05). Animals with the genotype GG had significantly higher back fat thickness (1.358 cm) than animals with the genotype GR (1.288 cm, P<0.05) and RR (1.286 cm, P<0.05). However, the genotypes had no significant association with ADG and days to 90kg. According to results of this study, a G allele of the G150R was found to have a significant effect on back fat thickness. It will be possible to use SNP markers on selected pigs to improve backfat thickness, an important economic trait.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.10
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• pp.1535-1541
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• 2018

Objective: In birds, three types of melatonin receptors (MTNR1A, MTNR1B, and MTNR1C) have been cloned. Previous researches have showed that three melatonin receptors played an essential role in reproduction and ovarian physiology. However, the association of polymorphisms of the three receptors with duck reproduction traits and egg quality traits is still unknown. In this test, we chose MTNR1A, MTNR1B, and MTNR1C as candidate genes to detect novel sequence polymorphism and analyze their association with egg production traits in Shaoxing duck, and detected their mRNA expression level in ovaries. Methods: In this study, a total of 785 duck blood samples were collected to investigate the association of melatonin receptor genes with egg production traits and egg quality traits using a direct sequencing method. And 6 ducks representing two groups (3 of each) according to the age at first eggs (at 128 days of age or after 150 days of age) were carefully selected for quantitative real-time polymerase chain reaction. Results: Seven novel polymorphisms (MTNR1A: g. 268C>T, MTNR1B: g. 41C>T, and g. 161T>C, MTNR1C: g. 10C>T, g. 24A>G, g. 108C>T, g. 363 T>C) were detected. The single nucleotide polymorphism (SNP) of MTNR1A (g. 268C>T) was significantly linked with the age at first egg (p<0.05). And a statistically significant association (p<0.05) was found between MTNR1C g.108 C>T and egg production traits: total egg numbers at 34 weeks old of age and age at first egg. In addition, the mRNA expression level of MTNR1A in ovary was significantly higher in late-mature group than in early-mature group, while MTNR1C showed a contrary tendency (p<0.05). Conclusion: These results suggest that identified SNPs in MTNR1A and MTNR1C may influence the age at first egg and could be considered as the candidate molecular marker for identify early maturely traits in duck selection and improvement.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.9
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• pp.1221-1225
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• 2005

The peroxisome proliferator-activated receptors (PPARs) are members of a superfamily of nuclear hormone receptors. Lots of studies in rodents and humans have shown that PPARs were involved in lipid metabolism and adipocyte differentiation. The main objective of this work was to detect the single nucleotide polymorphisms (SNPs) in whole coding regions of peroxisome proliferator-activated receptor alpha (PPAR-$\alpha$) and gamma (PPAR-$\gamma$) genes with approach of single strand conformation polymorphism (SSCP) in the chicken population of Arber Acres broiler, Hyline layer and three Chinese native breeds (Shiqiza, Beijing You, Bai'r). Two SNPs of C1029T and C297T were found in chicken PPAR-$\alpha$ and PPAR-$\gamma$ genes respectively and each SNP found three genotypes in the experimental populations. The results showed that the distribution frequency of 3 genotypes in Arber Acres broiler, Hyline layer and Chinese native breeds had significant differences on the PPAR-$\alpha$ and PPAR-$\gamma$ gene respectively (p<0.01). Furthermore, in the PPAR-$\alpha$ gene, the results of least square estimation for genotypes and body composition traits showed the BB genotype birds had higher abdominal fat weight (AFW) and percentage of abdominal fat (AFP) than AA genotype birds (p<0.05). From these we conjecture the PPAR-$\alpha$ and PPAR-$\gamma$ genes were suffered intensive selection during the long term commercial breeding and the PPAR-$\alpha$ gene may be a major gene or linked to the major genes that impact chicken fat metabolism and the SNPs could be used in molecular assistant selection (MAS) as a genetic marker for the chicken fatness traits.