• 한국가금학회지
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• 제43권4호
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• pp.263-272
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• 2016

한국 재래닭은 맛이나 기호성에서 한국 소비자들의 입맛에 적합한 것으로 알려져 있는데, 이러한 한국 재래닭의 특성을 결정짓는 유전적 요소들이 어떤 것들이 있는지 많이 밝혀지지 않았다. 본 연구에서는, 맛을 결정하는 요인 중 하나인 지질의 대사와 관련된 유전자들 내에 존재하는 nsSNP 연구를 통해서, 한국 재래닭의 유전적 특성을 설명하기 위한 자료를 확보하고자 분석을 실시하였다. 지질대사와 관련한 81개 유전자에 대하여 한국 재래닭에 공통으로 존재하는 nsSNP를 139개 동정하였으며, 이 중 9개의 유전자에 존재하는 14개의 nsSNP가 유해성 nsSNP로 확인되었다. 이들 9개 유전자에 대해 단백질 도메인 예측을 실시하였으며, 그 결과, 유해성 nsSNP들에 의해 바뀐 아미노산들이 모두 주요도메인의 외부에 존재함을 알 수 있었다. 이는 한국 재래닭에서 공통으로 발견한 nsSNP들이 유전자의 고유 기능에 큰 영향을 미치기 보다는 다소 미미한 변화를 통해 한국 재래닭 고유의 특성을 형성하는데 더 큰 역할을 한 것으로 사료된다. 이러한 부분들은 차후 실험을 통해 밝혀져야 할 부분이며, 한국 재래닭의 맛과 관련된 형질 개량을 위한 분자육종 기술 개발에 주요한 자료로 활용될 수 있을 것으로 기대되어진다.

• Animal Bioscience
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• 제37권3호
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• pp.428-436
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• 2024

Objective: This study compared five distinct sets of biological pathways and associated genes related to semen volume (VOL), number of sperm (NS), and sperm motility (MOT) in the Thai multibreed dairy population. Methods: The phenotypic data included 13,533 VOL records, 12,773 NS records, and 12,660 MOT records from 131 bulls. The genotypic data consisted of 76,519 imputed and actual single nucleotide polymorphisms (SNPs) from 72 animals. The SNP additive genetic variances for VOL, NS, and MOT were estimated for SNP windows of one SNP (SW1), ten SNP (SW10), 30 SNP (SW30), 50 SNP (SW50), and 100 SNP (SW100) using a single-step genomic best linear unbiased prediction approach. The fixed effects in the model were contemporary group, ejaculate order, bull age, ambient temperature, and heterosis. The random effects accounted for animal additive genetic effects, permanent environment effects, and residual. The SNPs explaining at least 0.001% of the additive genetic variance in SW1, 0.01% in SW10, 0.03% in SW30, 0.05% in SW50, and 0.1% in SW100 were selected for gene identification through the NCBI database. The pathway analysis utilized genes associated with the identified SNP windows. Results: Comparison of overlapping and non-overlapping SNP windows revealed notable differences among the identified pathways and genes associated with the studied traits. Overlapping windows consistently yielded a larger number of shared biological pathways and genes than non-overlapping windows. In particular, overlapping SW30 and SW50 identified the largest number of shared pathways and genes in the Thai multibreed dairy population. Conclusion: This study yielded valuable insights into the genetic architecture of VOL, NS, and MOT. It also highlighted the importance of assessing overlapping and non-overlapping SNP windows of various sizes for their effectiveness to identify shared pathways and genes influencing multiple traits.

• 생명과학회지
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• 제25권11호
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• pp.1304-1310
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• 2015

주기성 시계 유전자 3(period circadian clock gene 3, PER3)는 포유류에서 생물학적 주기 타이밍 시스템의 역할을 수행 한다. 이 유전자는 규칙적인 운동 체계에 의해 근육에서 전사 개시 되는 것으로 알려져 있다. 인간과 마우스에서는 본 유전자에 대해 잘 알려져 있지만, 주기 및 연주기 동안 낮의 길이에 영향을 많이 받는 말에서 운동 연관 연구는 존재하지 않는다. 운동 시 근육의 기능에 중요한 역할을 하는 PER3 유전자에 대해 대표적인 경주마인 국내산 더러브렛 품종의 운동 전과 운동 후 유전자 발현을 분석하기 위해 본 연구를 수행하였다. 그 결과, 골격근에서 PER3 유전자의 발현은 운동 전에 비해 운동 후에 유의적으로 증가하는 것으로 나타났다. 또한, 인실리코상에서 4개의 비동의성 단일 염기 변이(non-synonymous single nucleotide polymorphism, nsSNP) 분석과 이러한 nsSNP의 단백질 구조 및 기능 분석 결과, 전체 자유 에너지와 RMSD 값은 돌연변이의 원인이 될 수 있음으로 나타났다. 이 중, nsSNP–s395916798 (G72R)은 구조적 기능적 측면에서 중요한 잔기의 안정화 효과와 연관된 것을 알 수 있었다. 본 연구는 운동에 따라 더러브렛 골격근 내 PER3 발현 차이는 운동이라는 표현형에 대표될 수 있음을 확인하였다. 또한, SNP의 조합을 활용하여 운동 후 경주마의 조기 회복의 평가 지표로써 유용한 바이오마커가 될 수 있음을 시사한다.

• 한국동물생명공학회지
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• 제39권2호
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• pp.138-144
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• 2024

Background: As the number of households raising companion dogs increases, the pet genetic analysis market also continues to grow. However, most studies have focused on specific purposes or native breeds. This study aimed to collect genomic data through single nucleotide polymorphism (SNP) chip analysis of companion dogs in South Korea and perform genetic diversity analysis and SNP annotation. Methods: We collected samples from 95 dogs belonging to 26 breeds, including mixed breeds, in South Korea. The SNP genotypes were obtained for each sample using an Axiom^TM Canine HD Array. Quality control (QC) was performed to enhance the accuracy of the analysis. A genetic diversity analysis was performed for each SNP. Results: QC initially selected SNPs, and after excluding non-diverse ones, 621,672 SNPs were identified. Genetic diversity analysis revealed minor allele frequencies, polymorphism information content, expected heterozygosity, and observed heterozygosity values of 0.220, 0.244, 0.301, and 0.261, respectively. The SNP annotation indicated that most variations had an uncertain or minimal impact on gene function. However, approximately 16,000 non-synonymous SNPs (nsSNPs) have been found to significantly alter gene function or affect exons by changing translated amino acids. Conclusions: This study obtained data on SNP genetic diversity and functional SNPs in companion dogs raised in South Korea. The results suggest that establishing an SNP set for individual identification could enable a gene-based registration system. Furthermore, identifying and researching nsSNPs related to behavior and diseases could improve dog care and prevent abandonment.

• Genomics & Informatics
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• 제6권4호
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• pp.173-180
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• 2008

The human genome has evolved as a consequence of evolutionary forces, such as natural selection. In this study, we investigated natural selection on the human genes by comparing the numbers of nonsynonymous (NS) and synonymous (S) mutations in individual genes. We initially collected all coding SNP data of all human genes from the public dbSNP. Among the human genes, we selected 3 different selection groups of genes: positively selected genes (NS/S${\geq}$3), negatively selected genes (NS/S${\leq}$1/3) and neutral selection genes (0.9

• Asian-Australasian Journal of Animal Sciences
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• 제31권8호
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• pp.1150-1159
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• 2018

Objective: Non-synonymous single nucleotide polymorphisms (nsSNPs) were identified in Berkshire selective sweep regions and then were investigated to discover genetic nsSNP mechanisms that were potentially associated with Berkshire domestication and meat quality. We further used bioinformatics tools to predict damaging amino-acid substitutions in Berkshire-related nsSNPs. Methods: nsSNPs were examined in whole genome resequencing data of 110 pigs, including 14 Berkshire pigs, generated using the Illumina Hiseq2000 platform to identify variations that might affect meat quality in Berkshire pigs. Results: Total 65,550 nsSNPs were identified in the mapped regions; among these, 319 were found in Berkshire selective-sweep regions reported in a previous study. Genes encompassing these nsSNPs were involved in lipid metabolism, intramuscular fatty-acid deposition, and muscle development. The effects of amino acid change by nsSNPs on protein functions were predicted using sorting intolerant from tolerant and polymorphism phenotyping V2 to reveal their potential roles in biological processes that may correlate with the unique Berkshire meat-quality traits. Conclusion: Our nsSNP findings confirmed the history of Berkshire pigs and illustrated the effects of domestication on generic-variation patterns. Our novel findings, which are generally consistent with those of previous studies, facilitated a better understanding of Berkshire domestication. In summary, we extensively investigated the relationship between genomic composition and phenotypic traits by scanning for nsSNPs in large-scale whole-genome sequencing data.

• 한국축산식품학회지
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• 제37권6호
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• pp.926-930
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• 2017

High-quality meat is of great economic importance to the pig industry. The 1-acylglycerol-3-phosphate-O-acyltransferase 5 (AGPAT5) enzyme converts lysophosphatidic acid to phosphatidic acid in the mitochondrial membrane. In this study, we found that the porcine AGPAT5 gene was highly expressed in muscle tissue, influencing meat characteristics, and we also identified a non-synonymous single-nucleotide polymorphism (nsSNP) (rs196952262, c.673 A>G) in the gene, associated with a change of isoleucine 225 to valine. The presence of this nsSNP was significantly associated with meat color (lightness), lower cooking loss, and lower carcass temperatures 1, 4, and 12 h after slaughter (items T1, T4, and T12 on the recognized quality scale, respectively), and tended to increase backfat thickness and the water-holding capacity. These results suggest that nsSNP (c.673A>G) of the AGPAT5 gene is a potential genetic marker of high meat quality in pigs.

• BMB Reports
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• 제40권1호
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• pp.95-99
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• 2007

Bovine coding region single nucleotide polymorphisms located proximal to quantitative trait loci were identified to facilitate bovine QTL fine mapping research. A total of 692,763 bovine SNPs was extracted from 39,432 UniGene clusters, and 53,446 candidate SNPs were found to be a depth >3. In order to validate the in silico SNPs experimentally, 186 animals representing 14 breeds and 100 mixed breeds were analyzed. Genotyping of 40 randomly selected candidate SNPs revealed that 43% of these SNPs ranged in frequency from 0.009 to 0.498. To identify non-synonymous SNPs and to correct for possible frameshift errors in the ESTs at the predicted SNP positions, we designed a program that determines coding regions by protein-sequence referencing, and identified 17,735 nsSNPs. The SNPs and bovine quantitative traits loci informations were integrated into a bovine SNP data: BcSNPdb (http://snugenome.snu.ac.kr/BtcSNP/). Currently there are 43 different kinds of quantitative traits available. Thus, these SNPs would serve as valuable resources for exploiting genomic variation that influence economically and agriculturally important traits in cows.

• Asian-Australasian Journal of Animal Sciences
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• 제32권2호
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• pp.290-296
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• 2019

Objective: Pigs share many physiological, anatomical and genomic similarities with humans, which make them suitable models for biomedical researches. Understanding the genetic status of Yucatan miniature pigs (YMPs) and their association with human diseases will help to assess their potential as biomedical model animals. This study was performed to identify non-synonymous single nucleotide polymorphisms (nsSNPs) in selective sweep regions of the genome of YMPs and present the genetic nsSNP distributions that are potentially associated with disease occurrence in humans. Methods: nsSNPs in whole genome resequencing data from 12 YMPs were identified and annotated to predict their possible effects on protein function. Sorting intolerant from tolerant (SIFT) and polymorphism phenotyping v2 analyses were used, and gene ontology (GO) network and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses were performed. Results: The results showed that 8,462 genes, encompassing 72,067 nsSNPs were identified, and 118 nsSNPs in 46 genes were predicted as deleterious. GO network analysis classified 13 genes into 5 GO terms (p<0.05) that were associated with kidney development and metabolic processes. Seven genes encompassing nsSNPs were classified into the term associated with Alzheimer's disease by referencing the genetic association database. The KEGG pathway analysis identified only one significantly enriched pathway (p<0.05), hsa04080: Neuroactive ligand-receptor interaction, among the transcripts. Conclusion: The number of deleterious nsSNPs in YMPs was identified and then these variants-containing genes in YMPs data were adopted as the putative human diseases-related genes. The results revealed that many genes encompassing nsSNPs in YMPs were related to the various human genes which are potentially associated with kidney development and metabolic processes as well as human disease occurrence.

• Asian-Australasian Journal of Animal Sciences
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• 제31권3호
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• pp.309-315
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• 2018

Objective: This study aimed to test the expression patterns of ERBB receptor feedback inhibitor 1 (ERRFI1) before and after exercise and the association of non-synonymous single-nucleotide polymorphisms (nsSNPs) of horse ERRFI1 with racing traits in Thoroughbreds. Methods: We performed bioinformatics and gene expression analyses for horse ERRFI1. Transcription factor (TF) binding sites in the 5'-regulatory region of this gene were identified through a tool for prediction of TF-binding site (PROMO). A general linear model was used to detect the association between the nsSNP (LOC42830758 A to G) and race performance. Results: Quantitative polymerase chain reaction analysis showed that expression level of ERRFI1 after exercise was 1.6 times higher than that before exercise. Ten transcription factors were predicted from the ERRFI1 regulatory region. A novel nsSNP (LOC42830758 A to G) was found in ERRFI1, which was associated with three racing traits including average prize money, average racing index, and 3-year-old starts percentile ranking. Conclusion: Our analysis will be helpful as a basis for studying genes and SNPs that affect race performance in racehorses.