• Asian-Australasian Journal of Animal Sciences
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• 제31권1호
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• pp.13-18
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• 2018

Objective: Meat quality including muscle color in chickens is an important trait and continuous selective pressures for fast growth and high yield have negatively impacted this trait. This study was conducted to investigate genetic variations responsible for regulating muscle color. Methods: Whole genome re-sequencing analysis using Illumina HiSeq paired end read method was performed with pooled DNA samples isolated from two broiler chicken lines divergently selected for muscle color (high muscle color [HMC] and low muscle color [LMC]) along with their random bred control line (RAN). Sequencing read data was aligned to the chicken reference genome sequence for Red Jungle Fowl (Galgal4) using reference based genome alignment with NGen program of the Lasergene software package. The potential causal single nucleotide polymorphisms (SNPs) showing non-synonymous changes in coding DNA sequence regions were chosen in each line. Bioinformatic analyses to interpret functions of genes retaining SNPs were performed using the ingenuity pathways analysis (IPA). Results: Millions of SNPs were identified and totally 2,884 SNPs (1,307 for HMC and 1,577 for LMC) showing >75% SNP rates could induce non-synonymous mutations in amino acid sequences. Of those, SNPs showing over 10 read depths yielded 15 more reliable SNPs including 1 for HMC and 14 for LMC. The IPA analyses suggested that meat color in chickens appeared to be associated with chromosomal DNA stability, the functions of ubiquitylation (UBC) and quality and quantity of various subtypes of collagens. Conclusion: In this study, various potential genetic markers showing amino acid changes were identified in differential meat color lines, that can be used for further animal selection strategy.

• Journal of Animal Science and Technology
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• 제51권6호
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• pp.453-458
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• 2009

Prion protein (PRNP) is known to be a causative protein for transmissible spongiform encephalopathy (TSE), a disease occurring in human and animals. Previous results indicate that the genetic variability can affect the resistance and susceptibility of goat scrapie and can give the guideline for reducing the risk of this disease. Until now, 35 single nucleotide polymorphisms (SNPs) were identified in goat PRNP gene from many countries such as Great Britain, Italy, United States of America and Asian countries etc. In this study, SNPs in PRNP gene have been investigated to research the PRNP variations and their possible TSE risks in 60 Korean native goats. Based on the sequencing results, we identified four SNPs and three of those polymorphisms (G126A, C414T and C718T) were synonymous and the A428G polymorphism was non-synonymous which changes the amino acid histidine to arginine. Previously, all of these four SNPs were identified in Asian native goats. Specifically, five polymorphisms were identified in Asian native goats and two of them (G126A and C414T) were silent mutations, and the other SNPs (T304G, A428G and T718C) caused amino acid changes (W102G, H143R and S240P). Comparing with SNP results from other breeds, this study is an initial step to understand resistance and susceptibility of this disease in Korean native goats.

• Journal of Periodontal and Implant Science
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• 제42권5호
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• pp.151-157
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• 2012

Purpose: Cyclooxygenase (COX) enzyme catalyzes the production of prostaglandins, which are important mediators of tissue destruction in periodontitis. Single nucleotide polymorphisms of $COX_2$ enzyme have been associated with increasing susceptibility to inflammatory diseases. The present study evaluates the association of two single nucleotide polymorphisms in $COX_2$ gene (-1195G>A and $8_{473}$C>T) with chronic periodontitis in North Indians. Methods: Both SNPs and their haplotypes were used to explore the associations between $COX_2$ polymorphisms and chronic periodontitis in 56 patients and 60 controls. Genotyping was done by polymerase chain reaction followed by restriction fragment length polymorphism. Chi-square test and logistic regression analysis were performed for association analysis. Results: By the individual genotype analysis, mutant genotypes (GA and AA) of $COX_2$-1195 showed more than a two fold risk (odds ratio [OR]>2) and $COX_2$ $8_{473}$ (TC and CC) showed a reduced risk for the disease, but the findings were not statistically significant. Haplotype analysis showed that the frequency of the haplotype AT was higher in the case group and a significant association was found for haplotype AT (OR, 1.79; 95% confidence interval, 1.03 to 3.11; P=0.0370) indicating an association between the AT haplotype of $COX_2$ gene SNPs and chronic periodontitis. Conclusions: Individual genotypes of both the SNPs were not associated while haplotype AT was found to be associated with chronic periodontitis in North Indians.

• Asian-Australasian Journal of Animal Sciences
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• 제31권12호
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• pp.1980-1990
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• 2018

Objective: The aim of this study was to discover the functional impact of non-synonymous single nucleotide polymorphisms (nsSNPs) that were found in selective sweep regions of the Landrace genome Methods: Whole-genome re-sequencing data were obtained from 40 pigs, including 14 Landrace, 16 Yorkshire, and 10 wild boars, which were generated with the Illumina HiSeq 2000 platform. The nsSNPs in the selective sweep regions of the Landrace genome were identified, and the impacts of these variations on protein function were predicted to reveal their potential association with traits of the Landrace breed, such as reproductive capacity. Results: Total of 53,998 nsSNPs in the mapped regions of pigs were identified, and among them, 345 nsSNPs were found in the selective sweep regions of the Landrace genome which were reported previously. The genes featuring these nsSNPs fell into various functional categories, such as reproductive capacity or growth and development during the perinatal period. The impacts of amino acid sequence changes by nsSNPs on protein function were predicted using two in silico SNP prediction algorithms, i.e., sorting intolerant from tolerant and polymorphism phenotyping v2, to reveal their potential roles in biological processes that might be associated with the reproductive capacity of the Landrace breed. Conclusion: The findings elucidated the domestication history of the Landrace breed and illustrated how Landrace domestication led to patterns of genetic variation related to superior reproductive capacity. Our novel findings will help understand the process of Landrace domestication at the genome level and provide SNPs that are informative for breeding.

• Clinical and Experimental Reproductive Medicine
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• 제48권1호
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• pp.69-79
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• 2021

Objective: Poor ovarian response (POR) refers to a subnormal follicular response that leads to a decrease in the quality and quantity of the eggs retrieved after ovarian stimulation during assisted reproductive treatment (ART). The present study investigated the associations of multiple variants of the estrogen receptor 2 (ESR2) and follicle-stimulating hormone receptor (FSHR) genes with POR in infertile Jordanian women undergoing ART. Methods: Four polymorphisms, namely ESR2 rs1256049, ESR2 rs4986938, FSHR rs6165, and FSHR rs6166, were investigated in 60 infertile Jordanian women undergoing ART (the case group) and 60 age-matched fertile women (the control group), with a mean age of 33.60±6.34 years. Single-nucleotide polymorphisms (SNPs) were detected by restriction fragment length polymorphism and then validated using Sanger sequencing. Results: The p-value of the difference between the case and control groups regarding FSHR rs6166 was very close to 0.05 (p=0.054). However, no significant differences were observed between the two groups in terms of the other three SNPs, namely ESR2 rs1256049, ESR2 rs4986938, and FSHR rs6165 (p=0.561, p=0.433, and p=0.696, respectively). Conclusion: The association between FSHR rs6166 and POR was not statistically meaningful in the present study, but the near-significant result of this experiment suggests that statistical significance might be found in a future study with a larger number of patients.

• Asian-Australasian Journal of Animal Sciences
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• 제22권9호
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• pp.1241-1247
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• 2009

A large number of branded chicken products exist in Japan, and in some cases, the breed of chicken is an important factor used to attract consumer interest in the retail product. In order to establish a simple method for verifying such breed claims we applied the amplified fragment length polymorphism (AFLP) technique to nine chicken breeds (White Cornish, Red Cornish, White Plymouth Rock, New Hampshire, Rhode Island Red, Barred Plymouth Rock, Hinaidori, Tosajidori, Tsushimajidori) to search for molecular markers able to discriminate chicken breeds. Three breed-specific single nucleotide polymorphisms (SNP) were identified, one for each of Hinaidori, Tosajidori, or New Hampshire. A total of 219 individuals from the nine breeds were analyzed using a specific PCR test for each of these SNP. The PCR tests made it possible to discriminate between the breeds of chickens to identify products from these three breeds. This PCR method provides an efficient method for the routine analysis and verification of certified chicken products.

• Asian-Australasian Journal of Animal Sciences
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• 제31권8호
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• pp.1119-1126
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• 2018

Objective: Present investigation was aimed to study the Single Nucleotide Variants of the luteinizing hormone beta ($LH{\beta}$) gene and to analyze their association with the semen quality (fresh and post-thawed frozen semen) and luteinizing hormone (LH) concentrations in Murrah buffalo bulls. Methods: Polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) and Sanger sequencing method is used to study genetic variability in $LH{\beta}$ gene. LH assay was carried out using enzyme-linked immunosorbent assay method. A fixed general linear model was used to analyze association of single nucleotide polymorphism (SNP) of $LH{\beta}$ gene with semen quality in 109 and LH concentrations in 80 Murrah bulls. Results: $LH{\beta}$ gene was found to be polymorphic. Total six SNPs were identified in $LH{\beta}$ gene g C356090A, g C356113T, g A356701G, g G355869A, g G356330C, and g G356606T. Single Stranded Conformational Polymorphism variants of pattern 2 of exon 1+pattern 2 of exon 2+pattern 1 of exon 3 had highly significant (p<0.01) effect on sperm concentration (million/mL), percent mass motility, acrosome integrity and membrane integrity in fresh and frozen semen whereas significant (p<0.05) effect was observed on percent live spermatozoa. SSCP variants of pattern 2 of exon 1+pattern 2 of exon 2+pattern 1 of exon 3 had highly significant (p<0.01) effect on luteinizing hormone concentrations too. Conclusion: The observed association between SSCP variants of $LH{\beta}$ gene with semen quality parameters and LH concentrations indicated the possibilities of using $LH{\beta}$ as a candidate gene for identification of markers for semen quality traits and LH concentrations in Murrah buffaloes.

• Asian-Australasian Journal of Animal Sciences
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• 제20권7호
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• pp.1023-1029
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• 2007

Inhibins participate in the regulation of pituitary follicle-stimulating hormone synthesis and secretion, follicular maturation and steroidogenesis in the female. Inhibin ${\beta}_A$ gene (INHBA) was studied as a candidate gene for the prolificacy of sheep. Single nucleotide polymorphisms of the entire coding region and partial 3' untranslated region of INHBA were detected by PCR-SSCP in two high fecundity breeds (Small Tail Han and Hu sheep) and six low fecundity breeds (Dorset, Texel, German Mutton Merino, South African Mutton Merino, Chinese Merino and Corriedale sheep). Only the PCR products amplified by primers 3, 4 and 5 displayed polymorphisms. For primer 3, genotype CC was only detected in Chinese Merino sheep, genotype AA was detected in the other seven sheep breeds. Genotype BB was only detected in Hu sheep. Only Hu sheep displayed polymorphism. Eight or four nucleotide mutations were revealed between BB or CC and AA, respectively, and these mutations did not result in any amino acid change. For primer 4, genotypes EE, EG and GG were detected in Dorset and German Mutton Merino sheep, genotypes EE, EF and FF were detected in Chinese Merino sheep, only genotype EE was detected in the other five sheep breeds. Only Dorset, German Mutton Merino and Chinese Merino sheep displayed polymorphism. Sequencing revealed one nucleotide mutation ($114G{\rightarrow}A$) of exon 2 of INHBA gene between genotype FF and genotype EE, and this mutation did not cause any amino acid change. Another nucleotide change ($143C{\rightarrow}T$) was identified between genotype GG and genotype EE, and this mutation resulted in an amino acid change of $serine{\rightarrow}leucine$. For primer 5, genotypes KK and KL were detected in German Mutton Merino and Corriedale sheep, genotypes KK, LL and KL were detected in the other six sheep breeds. Genotype MM was only detected in Hu sheep. All of these eight sheep breeds displayed polymorphism. Sequencing revealed one nucleotide mutation ($218A{\rightarrow}G$) of exon 2 of the INHBA gene between genotype LL and genotype KK, and nine nucleotide mutations between genotype MM and genotype KK. These mutations did not alter amino acid sequence. The partial sequence (395 bp for exon 1 and 933 bp for exon 2) of the INHBA gene in Small Tail Han sheep (with genotype KK for primer 5) was submitted into GenBank (accession number EF192431). Small Tail Han sheep displayed polymorphisms only in the fragment amplified by primer 5. The Small Tail Han ewes with genotype LL had 0.53 (p<0.05) or 0.63 (p<0.05) more lambs than those with genotype KL or KK, respectively. The Small Tail Han ewes with genotype KL had 0.10 (p>0.05) more lambs than those with genotype KK.

• Journal of Animal Science and Technology
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• 제53권1호
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• pp.15-22
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• 2011

자돈의 생시 체중은 자돈의 이유 체중 및 생존율에도 크게 영향을 미친다. 또한 출하 시까지 돼지의 성장률 뿐만아니라 출하 일령 단축 및 출하 체중과도 밀접한 연관성이 있는 것으로 알려져 있다. 본 연구는 돼지 7번 염색체의 PGK 2 (phosphoglycerate kinase 2) 유전자의 promoter 영역 및 transcription 영역에 해당하는 DNA 염기서열을 유전체 구조분석을 통해 20개의 SNP (Single Nucleotide Polymorpism)를 발굴하였고, 발굴된 SNP 중 PGK 2 유전자의 전사 조절 영역 내 g.122 T>G 다형을 재래돼지와 Landrace를 이용한 $F_2$ 집단 268두 자돈의 성장 형질과의 연관성 분석을 실시한 결과, 생시 체중(p<0.01) 및 3주령 체중(p<0.001)에서 통계적으로 고도의 유의적 연관성이 있음을 확인 할 수 있었다. 따라서 본 연구를 통하여 확인된 PGK 2 유전자의 promoter 영역 내 성장 형질 관련 SNP는 건강한 자돈 및 종돈을 조기 선발하기 위한 유전자 marker로 활용 가능성을 제시하였다.

• 대한임상검사과학회지
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• 제55권2호
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• pp.93-104
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• 2023

이전 연구에서 83명의 한국인 폐선암 환자의 차세대 염기서열 분석법(next generation sequencing, NGS) 분석 결과 돌연변이 빈도가 높은 상위 5개 유전자 TP53 (60%), EGFR (48%), KRAS (14%), PIK3CA (8%), CDKN2A (6%)를 확인했다. 본연구는 NGS 분석을 이용하여 최근 한국인의 폐선암에서 돌연변이 발생 빈도가 높은 상위 5개 유전자에 대한 돌연변이 핫스팟을 분석하여 폐선암을 유발하는 새로운 표지자를 확인하고자 했으며 가장 많은 돌연변이가 발생한 TP53 유전자의 돌연변이 유형과 패턴을 폐암의 주요 원인인 흡연과의 연관성을 분석했으며 TP53 P72R SNP가 발생한 폐선암 환자의 임상병리학적 특성을 분석하고자 했다. TP53, EGFR, KRAS, PIK3CA, CDKN2A의 돌연변이 핫스팟을 분석한 결과 이전에 보고된 결과와 일치했으나 TP53의 경우 약간의 차이를 나타냈다. TP53 돌연변이 핫스팟은 DBD에 집중하여 발생하는 점은 기존 연구 결과와 같았으나 코돈 72에서 발생하는 높은 돌연변이 빈도는 이전에 보고된 연구 결과와 다르게 나타났다. TP53 돌연변이가 발생한 폐선암 환자의 임상 특성을 분석한 결과 남성보다 여성, 흡연자보다 비흡연자에게 더 많이 발생했다. 또한, TP53 돌연변이 유형은 흡연 여부와 상관없이 전환의 비율이 가장 높았으며 전환 또는 결실 그리고 전환과 결실이 동시에 발생하는 비율이 전이의 발생 비율보다 높게 나타났다. 한국인의 폐선암 증례에서 흡연 여부와 상관없이 가장 발생 빈도가 높은 돌연변이 핫스팟은 TP53 코돈 72 뉴클레오타이드 염기가 C에서 G로의 전환되어 아미노산이 proline에서 arginine으로 치환되는 TP53 P72R SNP 발생 비율이 가장 높게 나타났다. TP53 P72R SNP가 발생한 폐선암 증례들의 임상병리학적 특성을 분석한 결과 환자의 연령, 성별, 흡연 유무 그리고 종양의 분화도와 유의한 상관관계를 보이지 않았지만 낮은 병기와 유의한 상관관계를 나타냈다(P-value=0.026). 본연구는 NGS를 통해 한국인의 폐선암에서 돌연변이 발생 빈도가 가장 많이 보고되었던 EGFR이 아닌 TP53의 증가를 확인했고 그중에서도 흡연 여부와 관계없이 TP53 P72R SNP의 발생 빈도가 가장 높음을 보고하는 바이다.