• Asian-Australasian Journal of Animal Sciences
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• 제28권11호
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• pp.1545-1550
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• 2015

c-MYC (v-myelocytomatosis viral oncogene homologue) is a transcription factor that plays important role in many biological process including cell growth and differentiation, such as myogenesis and adipogenesis. In this study, we aimed to detect MYC gene polymorphisms, their genotype frequencies and to determine associations between these polymorphisms and meat quality traits in Berkshire pigs. We identified a single nucleotide polymorphism (SNP) in intron 2 of MYC gene by Sanger sequencing, i.e., g.3350G>C (rs321898326), that is only found in Berkshire pigs, but not in other breeds including Duroc, Landrace, and Yorkshire pigs that were used in this study. Genotypes of total 378 Berkshire pigs (138 sows and 240 boars) were determined using Hha I restriction enzyme digestion after polymerase chain reaction. Observed allele frequencies of GG, GC, and CC genotypes were 0.399, 0.508, and 0.093 respectively. Statistical analysis indicated that the g.3350G>C polymorphism was significantly associated with $pH_{45min}$ and cooking loss (p<0.05), suggesting that g.3350G>C SNP can be used for pre-selection of $pH_{45min}$ and cooking loss traits in Berkshire pigs.

• Genomics & Informatics
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• 제14권3호
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• pp.85-89
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• 2016

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that affects multiple organ systems. Although the etiology of SLE remains unclear, it is widely accepted that genetic factors could be involved in its pathogenesis. A number of genome-wide association studies (GWASs) have identified novel single-nucleotide polymorphisms (SNPs) associated with the risk of SLE in diverse populations. However, not all the SNP candidates identified from non-Asian populations have been validated in Koreans. In this study, we aimed to replicate the SNPs that were recently discovered in the GWAS; these SNPs have not been validated in Koreans or have only been replicated in Koreans with an insufficient sample size to conclude any association. For this, we selected five SNPs (rs1801274 in FCGR2A and rs2286672 in PLD2, rs887369 in CXorf21, rs9782955 in LYST, and rs3794060 in NADSYN1). Through the replication study with 656 cases and 622 controls, rs1801274 in FCGR2A was found to be significantly associated with SLE in Koreans (odds ratio, 1.26, 95% confidence interval, 1.06 to 1.50; p = 0.01 in allelic model). This association was also significant in two other models (dominant and recessive). The other four SNPs did not show a significant association. Our data support that FCGR polymorphisms play important roles in the susceptibility to SLE in diverse populations, including Koreans.

• Communications for Statistical Applications and Methods
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• 제26권1호
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• pp.1-9
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• 2019

Various probabilistic methods have been proposed for using interpopulation allele frequency differences to infer the ethnic group of a DNA specimen. The selection of the statistical method is critical because the accuracy of the statistical classification results vary. For the ancestry classification, we proposed a new ancestry evaluation method that estimate the combined ethnicity index as well as compared its performance with various classical classification methods using two real data sets. We selected 13 SNPs that are useful for the inference of ethnic origin. These single nucleotide polymorphisms (SNPs) were analyzed by restriction fragment mass polymorphism assay and followed by classification among ethnic groups. We genotyped 400 individuals from four ethnic groups (100 African-American, 100 Caucasian, 100 Korean, and 100 Mexican-American) for 13 SNPs and allele frequencies that differed among the four ethnic groups. Additionally, we applied our new method to HapMap SNP genotypes for 1,011 samples from 4 populations (African, European, East Asian, and Central-South Asian). Our proposed method yielded the highest accuracy among statistical classification methods. Our ethnic group classification system based on the analysis of ancestry informative SNP markers can provide a useful statistical tool to identify ethnic groups.

• Animal Bioscience
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• 제35권11호
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• pp.1635-1648
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• 2022

Thermal stress due to extreme changes in the thermal environment is a critical issue in cattle production. Many previous findings have shown a decrease in feed intake, milk yield, growth rate, and reproductive efficiency of cattle when subjected to thermal stress. Therefore, selecting thermo-tolerant animals is the primary goal of the efficiency of breeding programs to reduce those adverse impacts. The recent advances in molecular genetics have provided significant breeding advantages that allow the identification of molecular markers in both beef and dairy cattle breeding, including marker-assisted selection (MAS) as a tool in selecting superior thermo-tolerant animals. Single-nucleotide polymorphisms (SNPs), which can be detected by DNA sequencing, are desirable DNA markers for MAS due to their abundance in the genome's coding and non-coding regions. Many SNPs in some genes (e.g., HSP70, HSP90, HSF1, EIF2AK4, HSBP1, HSPB8, HSPB7, MYO1A, and ATP1A1) in various breeds of cattle have been analyzed to play key roles in many cellular activities during thermal stress and protecting cells against stress, making them potential candidate genes for molecular markers of thermotolerance. This review highlights the associations of SNPs within these genes with thermotolerance traits (e.g., blood biochemistry and physiological responses) and suggests their potential use as MAS in thermotolerant cattle breeding.

• Animal Bioscience
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• 제36권9호
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• pp.1357-1366
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• 2023

Objective: This study aimed to identify the single-nucleotide polymorphisms (SNPs) in the dual-specificity phosphatase 8 (DUSP8) and insulin-like growth factor 2 (IGF2) genes and to explore their effects on inosine-5'-monophosphate (IMP), inosine, and hypoxanthine contents in Korean native chicken -red-brown line (KNC-R Line). Methods: A total sample of 284 (males, n = 127; females n = 157) and 230 (males, n = 106; females, n = 124) aged of 10 weeks old KNC-R line was used for genotyping of DUSP8 and IGF2 genes, respectively. One SNP (rs313443014 C>T) in DUSP8 gene and two SNPs (rs315806609A/G and rs313810945T/C) in IGF2 gene were used for genotyping by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and KASP methods, respectively. The Two-way analysis of variance of the R program was used to associate DUSP8 and IGF2 genotypes with nucleotide contents in KNC-R chickens. Results: The DUSP8 (rs313443014 C>T) was polymorphic in KNC-R line and showed three genotypes: CC, CT, and TT. The IGF2 gene (rs315806609A/G and rs313810945T/C) was also polymorphic and had three genotypes per SNP, including GG, AG, and AA for the SNP rs315806609A/G and genotypes: CC, CT, and TT for the SNP rs313810945T/C. Association resulted into a strong significant association (p<0.01) with IMP, inosine, and hypoxanthine. Moreover, the significant effect of sex (p<0.05) on nucleotide content was also observed. Conclusion: The SNPs in the DUSP8 and IGF2 genes might be used as genetic markers in the selection and production of chickens with highly flavored meat.

• BMB Reports
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• 제39권2호
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• pp.183-188
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• 2006

Using the Phred/Phrap/Polyphred/Consed pipeline established in the National Livestock Research Institute of Korea, we predicted candidate coding single nucleotide polymorphisms (cSNPs) from 7,600 expressed sequence tags (ESTs) derived from three cDNA libraries (liver, M. longissimus dorsi, and intermuscular fat) of Hanwoo (Korean native cattle) steers. From the 7,600 ESTs, 829 contigs comprising more than two EST reads were assembled using the Phrap assembler. Based on the contig analysis, 201 candidate cSNPs were identified in 129 contigs, in which transitions (69%) outnumbered transversions (31%). To verify whether the predicted cSNPs are real, 17 SNPs involved in lipid and energy metabolism were selected from the ESTs. Twelve of these were confirmed to be real while five were identified as artifacts, possibly due to expressed sequence tag sequence error. Further analysis of the 12 verified cSNPs was performed using the program BLASTX. Five were identified as nonsynonymous cSNPs, five were synonymous cSNPs, and two SNPs were located in 3'-UTRs. Our data indicated that a relatively high SNP prediction rate (71%) from a large EST database could produce abundant cSNPs rapidly, which can be used as valuable genetic markers in cattle.

• Asian-Australasian Journal of Animal Sciences
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• 제30권1호
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• pp.8-19
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• 2017

Objective: A whole genome association study was conducted to identify single nucleotide polymorphisms (SNPs) with additive and dominant effects for growth and carcass traits in Korean native cattle, Hanwoo. Methods: The data set comprised 61 sires and their 486 Hanwoo steers that were born between spring of 2005 and fall of 2007. The steers were genotyped with the 35,968 SNPs that were embedded in the Illumina bovine SNP 50K beadchip and six growth and carcass quality traits were measured for the steers. A series of lack-of-fit tests between the models was applied to classify gene expression pattern as additive or dominant. Results: A total of 18 (0), 15 (3), 12 (8), 15 (18), 11 (7), and 21 (1) SNPs were detected at the 5% chromosome (genome) - wise level for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area (LMA) and marbling score, respectively. Among the significant 129 SNPs, 56 SNPs had additive effects, 20 SNPs dominance effects, and 53 SNPs both additive and dominance effects, suggesting that dominance inheritance mode be considered in genetic improvement for growth and carcass quality in Hanwoo. The significant SNPs were located at 33 quantitative trait locus (QTL) regions on 18 Bos Taurus chromosomes (i.e. BTA 3, 4, 5, 6, 7, 9, 11, 12, 13, 14, 16, 17, 18, 20, 23, 26, 28, and 29) were detected. There is strong evidence that BTA14 is the key chromosome affecting CWT. Also, BTA20 is the key chromosome for almost all traits measured (WWT, YWT, LMA). Conclusion: The application of various additive and dominance SNP models enabled better characterization of SNP inheritance mode for growth and carcass quality traits in Hanwoo, and many of the detected SNPs or QTL had dominance effects, suggesting that dominance be considered for the whole-genome SNPs data and implementation of successive molecular breeding schemes in Hanwoo.

• Asian-Australasian Journal of Animal Sciences
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• 제21권2호
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• pp.155-160
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• 2008

Several studies have reported quantitative trait loci (QTL) for meat quality on porcine chromosome 2 (http://www.animalgenome.org/QTLdb/pig.html). For application of the molecular genetic information to the pig industry through marker-assisted selection, single nucleotide polymorphism (SNP) markers were analyzed by comparative re-sequencing of polymerase chain reaction (PCR) products of 13 candidate genes with DNA from commercial pig breeds such as Berkshire, Yorkshire, Landrace, Duroc and Korean Native pig. A total of 34 SNPs were identified in 15 PCR products producing an average of one SNP in every 253 bp. PCR restriction fragment length polymorphism (RFLP) assays were developed for 11 SNPs and used to investigate allele frequencies in five commercial pig breeds in Korea. Eight of the SNPs appear to be fixed in at least one of the five pig breeds, which indicates that different selection among pig breeds might be applied to these SNPs. Polymorphisms detected in the PTH, CSF2 and FOLR genes were chosen to genotype a Berkshire-Yorkshire pig breed reference family for linkage and association analyses. Using linkage analysis, PTH and CSF2 loci were mapped to pig chromosome 2, while FOLR was mapped to pig chromosome 9. Association analyses between SNPs in the PTH, CSF2 and FOLR suggested that the CSF2 MboII polymorphism was significantly associated with several pork quality traits in the Berkshire and Yorkshire crossed F2 pigs. Our current findings provide useful SNP marker information to fine map QTL regions on pig chromosome 2 and to clarify the relevance of SNP and quantitative traits in commercial pig populations.

• 한국축산식품학회지
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• 제33권6호
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• pp.715-722
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• 2013

Heugu (Korea Black Cattle) is one of the indigenous cattle breeds in Korea; however there has been severe lack of genomic studies on the breed. In this study, we report the first whole genome resequencing of Heugu at higher sequence coverage using Illumina HiSeq 2000 platform. More than 153.6 Giga base pairs sequence was obtained, of which 97% of the reads were mapped to the bovine reference sequence assembly (UMD 3.1). The number of non-redundantly mapped sequence reads corresponds to approximately 28.9-fold coverage across the genome. From these data, we identified a total of over six million single nucleotide polymorphisms (SNPs), of which 29.4% were found to be novel using the single nucleotide polymorphism database build 137. Extensive annotation was performed on all the detected SNPs, showing that most of SNPs were located in intergenic regions (70.7%), which is well corresponded with previous studies. Of the total SNPs, we identified substantial numbers of non-synonymous SNPs (13,979) in 5,999 genes, which could potentially affect meat quality traits in cattle. These results provide genome-wide SNPs that can serve as useful genetic tools and as candidates in searches for phenotype-altering DNA difference implicated with meat quality traits in cattle. The importance of this study can be further pronounced with the first whole genome sequencing of the valuable local genetic resource to be used in further genomic comparison studies with diverse cattle breeds.

• Asian-Australasian Journal of Animal Sciences
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• 제29권11호
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• pp.1541-1546
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• 2016

Four carcass traits, namely carcass weight (CW), eye muscle area (EMA), back fat thickness (BF), and marbling score (MS), are the main price decision parameters used for purchasing Hanwoo beef. The development of DNA markers for these carcass traits for use in a beef management system could result in substantial profit for beef producers in Korea. The objective of this study was to validate the association of highly significant single nucleotide polymorphisms (SNPs) identified in a previous genome-wide association study (GWAS) with the four carcass traits in a commercial Hanwoo population. We genotyped 83 SNPs distributed across all 29 autosomes in 867 steers from a Korean Hanwoo feedlot. Six SNPs, namely ARS-BFGL-NGS-22774 (Chr4, Pos:4889229), ARS-BFGL-NGS-100046 (Chr6, Pos:61917424), ARS-BFGL-NGS-39006 (Chr27, Pos:38059196), ARS-BFGL-NGS-18790 (Chr10, Pos:26489109), ARS-BFGL-NGS-43879 (Chr9, Pos:39964297), and BTB-00775794 (Chr20, Pos:20476265), were found to be associated with CW, EMA, BF, and MS. The ARS-BFGL-NGS-22774, BTB-00775794, and ARS-BFGL-NGS-39006 markers accounted for 1.80%, 1.72%, and 1.35% (p<0.01), respectively, of the phenotypic variance in the commercial Hanwoo population. Many genes located in close proximity to the significant SNPs identified in this study were previously reported to have roles in carcass traits. The results of this study could be useful for marker-assisted selection programs.