• Journal of Life Science
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• v.17 no.11
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• pp.1505-1510
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• 2007

We found 8 single nucleotide polymorphisms (SNPs) in adipocyte fatty acid bonding protein (FABP4) gene as candidate gene of FAT1 locus on pig chromosome 4. With over 800 heads of major commercial pig breeds including Duroc, Landrace, Berkshire and Yorkshire, we analyzed SNPs of FABP4 gene to determine possible effects of FABP4 genotype to economically important traits. $400{\sim}800\;bp$ amplicons in FABP4 gene were used PCR-RFLP for each SNPs and we found that the frequency of some SNPs of this gene was different among the breeds. According to the statistical analyses to determine possible associations of each genotype with economic traits, it was found that subgroup with different genotypes showed significant differences in daily gain, backfat thickness, lean percentage and feed conversion ratio (P<0.05). Thus, as a Part of enhancing the selection competence related to swine growth rate and lean percentage, it is expected that FABP4 gene markers verified in this study will be useful to use for Korean commercial pig industry.

• ANNALS OF ANIMAL RESOURCE SCIENCES
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• v.29 no.4
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• pp.150-157
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• 2018

The Zygote arrest 1 (ZAR1) gene is known to affect early embryonic development in various vertebrates. In this study, we performed the association analysis to check whether there is any significant relationship between semen kinematic characteristics and the ZAR1 gene. To determine semen kinematic characteristics, we measured motility (MOT), straight-line velocity (VSL), curvilinear velocity (VCL), average path velocity (VAP), linearity (LIN), straightness (STR), amplitude of lateral head displacement (ALH), and beat cross frequency (BCF) of spermatozoa in boars. In order to detect single nucleotide polymorphisms (SNPs), we extracted genomic DNA from multiple Duroc boars, and then subsequently used them in sequencing reactions. As a result, three SNPs were detected in the intronic region of ZAR1 gene (g.2435T>C in intron 2, g.2605G>A and g.4633A>C in intron 3 ). SNPs g.2435T>C and g.2605G>A were significantly associated with MOT (p<0.01) and VSL (p<0.05), and g.4633A

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.3
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• pp.327-334
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• 2018

Objective: The objective of the present study was to validate genes and genomic regions associated with carcass weight using a low-density single nucleotide polymorphism (SNP) Chip in Hanwoo cattle breed. Methods: Commercial Hanwoo steers (n = 220) were genotyped with 20K GeneSeek genomic profiler BeadChip. After applying the quality control of criteria of a call rate ${\geq}90%$ and minor allele frequency (MAF) ${\geq}0.01$, a total of 15,235 autosomal SNPs were left for genome-wide association (GWA) analysis. The GWA tests were performed using single-locus mixed linear model. Age at slaughter was fitted as fixed effect and sire included as a covariate. The level of genome-wide significance was set at $3.28{\times}10^{-6}$ (0.05/15,235), corresponding to Bonferroni correction for 15,235 multiple independent tests. Results: By employing EMMAX approach which is based on a mixed linear model and accounts for population stratification and relatedness, we identified 17 and 16 loci significantly (p<0.001) associated with carcass weight for the additive and dominant models, respectively. The second most significant (p = 0.000049) SNP (ARS-BFGL-NGS-28234) on bovine chromosome 4 (BTA4) at 21 Mb had an allele substitution effect of 43.45 kg. Some of the identified regions on BTA2, 6, 14, 22, and 24 were previously reported to be associated with quantitative trait loci for carcass weight in several beef cattle breeds. Conclusion: This is the first genome-wide association study using SNP chips on commercial Hanwoo steers, and some of the loci newly identified in this study may help to better DNA markers that determine increased beef production in commercial Hanwoo cattle. Further studies using a larger sample size will allow confirmation of the candidates identified in this study.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.9
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• pp.1256-1264
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• 2016

Adrenergic, alpha-1B-, receptor (ADRA1B) and peroxisome proliferator-activated receptor gamma, coactivator 1 beta (PPARGC1B) genes are involved in regulation of hen ovarian development. In this study, these two genes were investigated as possible molecular markers associated with hen-housed egg production, egg weight (EW) and body weight in Chinese Dagu hens. Samples were analyzed using the polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) technique, followed by sequencing analysis. Two novel single nucleotide polymorphisms (SNPs) were identified within the candidate genes. Among them, an A/G transition at base position 1915 in exon 2 of ADRA1B gene and a T/C mutation at base position 6146 in the 3'- untranslated region (UTR) of PPARGC1B gene were found to be polymorphic and named SNP A1915G and T6146C, respectively. The SNP A1915G (ADRA1B) leads to a non-synonymous substitution (aspartic acid 489-to-glycine). The 360 birds from the Dagu population were divided into genotypes AA and AG, allele A was found to be present at a higher frequency. Furthermore, the AG genotype correlated with significantly higher hen-housed egg production (HHEP) at 30, 43, 57, and 66 wks of age and with a higher EW at 30 and 43 wks (p<0.05). For the SNP T6146C (PPARGC1B), the hens were typed into TT and TC genotypes, with the T allele shown to be dominant. The TC genotype was also markedly correlated with higher HHEP at 57 and 66 wks of age and EW at 30 and 43 wks (p<0.05). Moreover, four haplotypes were reconstructed based on these two SNPs, with the AGTC haplotype found to be associated with the highest HHEP at 30 to 66 wks of age and with higher EW at 30 and 43 wks (p<0.05). Collectively, the two SNPs identified in this study might be used as potential genetic molecular markers favorable in the improvement of egg productivity in chicken breeding.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.6
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• pp.784-790
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• 2018

Objective: The genetic effects of an individual on the phenotypes of its social partners, such as its pen mates, are known as social genetic effects. This study aims to identify the candidate genes for social (pen-mates') average daily gain (ADG) in pigs by using the genome-wide association approach. Methods: Social ADG (sADG) was the average ADG of unrelated pen-mates (strangers). We used the phenotype data (16,802 records) after correcting for batch (week), sex, pen, number of strangers (1 to 7 pigs) in the pen, full-sib rate (0% to 80%) within pen, and age at the end of the test. A total of 1,041 pigs from Landrace breeds were genotyped using the Illumina PorcineSNP60 v2 BeadChip panel, which comprised 61,565 single nucleotide polymorphism (SNP) markers. After quality control, 909 individuals and 39,837 markers remained for sADG in genome-wide association study. Results: We detected five new SNPs, all on chromosome 6, which have not been associated with social ADG or other growth traits to date. One SNP was inside the prostaglandin $F2{\alpha}$ receptor (PTGFR) gene, another SNP was located 22 kb upstream of gene interferon-induced protein 44 (IFI44), and the last three SNPs were between 161 kb and 191 kb upstream of the EGF latrophilin and seven transmembrane domain-containing protein 1 (ELTD1) gene. PTGFR, IFI44, and ELTD1 were never associated with social interaction and social genetic effects in any of the previous studies. Conclusion: The identification of several genomic regions, and candidate genes associated with social genetic effects reported here, could contribute to a better understanding of the genetic basis of interaction traits for ADG. In conclusion, we suggest that the PTGFR, IFI44, and ELTD1 may be used as a molecular marker for sADG, although their functional effect was not defined yet. Thus, it will be of interest to execute association studies in those genes.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.9
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• pp.5415-5420
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• 2013

Background: Cell cycle deregulation is a major component of carcinogenesis. The p53 tumor suppressor gene plays an important role in regulating cell cycle arrest, and mouse double minute 2 (MDM2) is a key regulator of p53 activity and degradation. Abnormal expression of p53 and MDM2 occurs in various cancers including lung cancer. Methods: We investigated the distribution of the p53 Arg72Pro (rs1042522) and MDM2 SNP309 (rs2279744) genotypes in patients and healthy control subjects to assess whether these single nucleotide polymorphisms (SNPs) are associated with an increased risk of lung adenocarcinomas in Chinese female non-smokers. Genotypes of 764 patients and 983 healthy controls were determined using the TaqMan SNP genotyping assay. Results: The p53 Pro/Pro genotype (adjusted OR = 1.55, 95% CI = 1.17-2.06) significantly correlated with an increased risk of lung adenocarcinoma, compared with the Arg/Arg genotype. An increased risk was also noted for MDM2 GG genotype (adjusted OR = 1.68, 95% CI = 1.27-2.21) compared with the TT genotype. Combined p53 Pro/Pro and MDM2 GG genotypes (adjusted OR = 2.66, 95% CI = 1.54-4.60) had a supermultiplicative interaction with respect to lung adenocarcinoma risk. We also found that cooking oil fumes, fuel smoke, and passive smoking may increase the risk of lung adenocarcinomas in Chinese female non-smokers who carry p53 or MDM2 mutant alleles. Conclusions: P53 Arg72Pro and MDM2 SNP309 polymorphisms, either alone or in combination, are associated with an increased lung adenocarcinoma risk in Chinese female non-smokers.

• Journal of Life Science
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• v.14 no.2
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• pp.275-279
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• 2004

Gene polymorphisms of cytokines and their receptors are attractive candidates as genetic factors in the pathogenesis of immune-mediated diseases and have been reported to be associated with disease susceptibility to autoimmune, inflammatory and infectious diseases. IL-29 is one of important candidate genes for complex trait of genetic diseases but there is no published survey of single nucleotide polymorphisms (SNPs) in this gene. In this study, for the first time, we have examined the full genomic sequence of IL-29 including the promoter regions to identify SNPs. We examined the frequencies of genotypes and alleles at the SNP site of IL-29 in allergic rhinitis patients and non-allergic rhinitis controls using the direct sequencing method to determine whether this IL-29 SNP is associated with allergic rhinitis in Korean population. We identified one novel SNP (1184C＞A) in the intron 2 and one novel variation site (-1842_-1841dupGA) in the promoter region of human IL-29 gene. The P values of SNP or variation site were not significant between the healthy controls and allergic rhinitis patients. Our results suggest that the 1184C＞A polymorphism and -1842_-1841dupGA variation site in human IL-29 gene were not associated to allergic rhinitis.

• Korean Journal of Breeding Science
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• v.42 no.5
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• pp.507-514
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• 2010

Peanut(Arachis hypogaea L.) is one of the major oilseed crops. The peanut oil consists of palmitic, oleic and linoleic acids, which are present at levels of 10%, 36-67% and 15-43%, respectively. High oleate mutant of peanut F435 contains 80% oleate and as little as 2% linoleate in seed oil. Previous study indicated that delta 12 fatty acid desaturase is a major enzyme controlling the oleate content in seeds of oilseed crops. F435 sequence alignment of their coding regions disclosed that an extra A(adenine) was inserted at the position +2,823 bp of delta 12 fatty acid desaturase gene. This study was to develop molecular marker (SNP marker) co-segregating with the high oleate trait. Chopyeong ${\times}$ F435 $F_2$ 41 population were investigated using molecular marker and fatty acid assay (NIR and gas chromatography). Finally, this marker segregates Chopyeong type 26 lines, heterotype 9 lines and F435 type 6 lines. These results in our study suggested that SNP marker conform fatty acid assay.

• Korean journal of applied entomology
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• v.59 no.3
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• pp.217-231
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• 2020

In 2019, the sex pheromones of Spodoptera frugiperda were used to examine moth trapping in cornfields in Gochang, Korea. Four types of traps were prepared, two funnel-types and two delta-types, each baited with 300 or 1000 ㎍ of a two-component (2C) blend of synthetic sex pheromones [100% (Z)-9-tetradecenyl acetate (Z9-14Ac) and 2% (Z)-7-dodecenyl acetate (Z7-12Ac)]. The greatest number of S. frugiperda were captured in the 300 ㎍ funnel-type trap (first catch: August 6). Large numbers of Mythimna loreyi (a non-target) were also caught in the funnel-type traps. Two wing-type traps were baited with 1000 ㎍ of the 2C blend or a four-component (4C) blend [100% (Z)-9-tetradecenyl acetate, 8% (Z)-11-hexadecenyl acetate (Z11-16Ac), 2% (Z)-7-dodecenyl acetate, and 1% (Z)-9-dodecenyl acetate (Z9-12Ac)] and the capture efficiency was assessed. Low numbers of S. frugiperda were captured regardless of the blend, and more M. loreyi were captured using the 4C blend. The two intraspecies groups clustered separately in a phylogenetic tree constructed using partial sequences (1004 bp) of cytochrome c oxidase subunit 1 (CO1). Of the 70 S. frugiperda captured in the pheromone traps, 66 belonged to CO1-RS (CO1 rice-strain) and 4 to CO1-CS (CO1 corn-strain). Twelve consistent single nucleotide polymorphisms (SNPs) were identified in CO1 between the CO1-RS and CO1-CS groups of S. frugiperda. Of the 73 S. frugiperda, 4 had the same SNP pattern as the CO1-CS group (including the corn strain) and 69 had the same SNP pattern as the CO1-RS group (including the rice strain).

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.5
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• pp.643-649
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• 2018

Objective: POU class 1 homeobox 1 (POU1F1) mediates growth hormone expression and activity by altering transcription, eventually resulting in growth rate variations. Therefore, we aimed to identify chicken POU1F1 polymorphisms and evaluate the association between single nucleotide polymorphisms (SNPs) and growth-related traits, and logistic growth curve parameter traits (${\alpha}$, ${\beta}$, and ${\gamma}$). Methods: Three SNPs (M_1 to M_3) were used to genotype 585 $F_1$ and 88 $F_0$ birds from five Korean native chicken lines using a polymerase chain reaction-restriction fragment length polymorphism method. Results: Single marker analyses and traits association analyses showed that M_2 was significantly associated with body weight at two weeks, weight gain from hatch to 2 weeks, and weight gain from 16 to 18 weeks (p<0.05). M_3 was significantly associated with weight gain from 14 to 16 weeks and from 16 to 18 weeks, and asymptotic body weight (${\alpha}$) (p<0.05). No traits were associated with M_1. The POU1F1 haplogroups were significantly associated with weight gain from 14 to 16 weeks (p = 0.020). Linkage disequilibrium test and Haploview analysis shown one main haploblock between M_2 and M_3 SNP. Conclusion: Thus, POU1F1 significantly affects the growth of Korean native chickens and their growth curve traits.