• Korean Journal of Poultry Science
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• v.43 no.4
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• pp.263-272
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• 2016

In this study, we aimed to identify the nonsynonymous single nucleotide polymorphisms (nsSNPs) located in lipid metabolism-related genes because lipids are an important factor affecting the taste and flavor of meat, and they predict the functional consequences. The results showed that we identified 139 common nsSNPs in all five Korean native chicken (KNC) lines from the 81 genes related to lipid metabolism. Furthermore, sorting intolerant from tolerant (SIFT) and polymorphism phenotyping v2 (Polyphen-2) analyses predicted that among the genes, 14 nsSNPs of nine genes might be deleterious. Protein domain prediction of the nine genes revealed that all deleterious nsSNPs identified in this study were located outside the functional domain. This observation suggests that the common deleterious nsSNPs might be dispensable and have a minor effect on the traits of the KNCs.

• Animal Bioscience
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• v.37 no.3
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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.

• Journal of Life Science
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• v.25 no.11
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• pp.1304-1310
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• 2015

The period circadian clock gene 3 (PER3) plays a role in the mammalian circadian clocksystem. A regular exercise regime may affect the PER3 transcription in skeletal muscle. Although the effects of day length on circadian and circannual processes are well established in humans and mice, the influence of exercise on these processes in the horse has not been investigated. The present study investigated the expression of the PER3 gene following exercise in a thoroughbred breed of Korean horse. In addition, a comprehensive in silico nonsynonymous single nucleotide polymorphism (nsSNP) analysis of the horse PER3 gene and predicted effects of nsSNPs on proteins were examined. The expression of PER3 in skeletal muscle was significantly upregulated after exercise. Four nsSNPs were functionally annotated and analyzed by computational prediction. The total free energy and RMSD values of PER3 gene showed causative mutations. The results showed that nsSNP s395916798 (G72R) was associated with residues that have stabilizing effects on structure and function of PER3 gene. This study documented role of PER3 gene in phenotypic adaptation related to exercise in skeletal muscle. Further, the SNPs in PER3 could serve as useful biomarkers of early recovery after exercise in racehorses.

• Genomics & Informatics
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• v.6 no.4
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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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• v.31 no.8
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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.

• Food Science of Animal Resources
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• v.37 no.6
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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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• v.40 no.1
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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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• v.32 no.2
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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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• v.31 no.3
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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.

• Korean Journal of Food Science and Technology
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• v.50 no.5
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• pp.480-485
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• 2018

In this study, to identify single nucleotide polymorphisms (SNPs) associated with meat quality in Berkshire pigs, we performed RNA sequencing. A non-synonymous SNP (nsSNP) in the Complement component 9 (C9) gene was identified, and the association between meat quality traits and the C9 genotype was analyzed. The nsSNP in the C9 gene was located at c.942 G>T. In the dominant model, significant associations were observed between the SNP and meat quality traits such as CIE L, collagen content, moisture level, and $pH_{24h}$, whereas in the co-dominant model, significant associations were observed between the SNP and CIE L, collagen content, and protein content. In the recessive model, a significant association between the C9 genotype and the collagen content was observed. In addition, we identified the significant relationship between the C9 genotype and meat quality according to sex. These results indicate that the C9 SNP can be used as a genetic marker for improving pork quality.