• Asian-Australasian Journal of Animal Sciences
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• v.19 no.3
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• pp.324-328
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• 2006

Carbonic anhydrase III (CA3) is a member of a multigene family that encode carbonic anhydrase isozymes. In this study, a complete coding sequence of the pig CA3 gene which encodes a 260 amino-acid protein was determined. The amino acid comparison showed high sequence similarities with previously identified human (86.5%) CA3 gene and mouse (91.5%) Car3 gene. The partial genomic DNA sequences were also investigated. The length of intron 1 was 727 bp. Comparative sequencing of three pig breeds revealed that there was a T${\rightarrow}$C substitution at position 363 within intron 1. The substitution was situated within a NcoI recognition site and was developed as a PCR-restriction fragment length polymorphism (RFLP) marker for further use in population variation investigations and association analysis. Two alleles (A and B) were identified, and 617 bp fragments were observed for the AA genotype and 236 bp and 381 bp fragments for the BB genotype. The polymorphism of CA3 was detected in 8 pig breeds. Allele B was predominant in the Western pig breeds. In addition, association studies of the CA3 polymorphism with carcass traits in 140 $Yorkshire{\times}Meishan$ $F_2$ offspring showed that the NcoI PCR- RFLP genotype may be associated with variation in several carcass traits of interest for pig breeding. Allele B was associated with increases in lean meat percentage, loin eye height and loin eye area. Statistically significant association with backfat thickness was also found; pigs with the AB genotype had much less backfat thickness than AA or BB genotypes.

• Animal Bioscience
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• v.36 no.6
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• pp.840-850
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• 2023

Objective: This study aimed to investigate the polymorphisms of the dopa decarboxylase (DDC) gene and association analysis with lamb quality and expression quantification of the DDC gene in phenotypically divergent Indonesian sheep. Methods: The totals of 189 rams with an average body weight of 24.12 kg at 10 to 12 months were used to identify DDC gene polymorphism using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Among 189 rams, several rams representing various sheep genotypes were used for an association study between genotypes and phenotypic traits with proc general linear model (GLM) analysis. In addition, the gene expression analysis of the DDC mRNA in the phenotypically divergent sheep population was analyzed using quantitative reverse-transcription PCR. Results: The DDC gene (g. 5377439 G>A) showed polymorphisms that indicated three genotypes: AA, AG, and GG. The DDC gene polymorphism was significantly associated (p≤0.05) with carcass characteristics including carcass percentage, carcass length, hot and cold carcass; physical properties of lamb quality including pH value; retail cut carcass; fatty acid composition such as fat content, pentadecanoic acid (C15:0), tricosylic acid (C23:0), lignoceric acid (C24:0), oleic acid (C18:1n9c), elaidic acid (C18:1n9t), nervonic acid (C24:1), linoleic acid (C18:2n6c), arachidonic acid (C20:4n6), cervonic acid (C22:6n3); and mineral content including potassium (K). The GG genotype of the DDC gene had the best association with lamb quality traits. The DDC gene expression analysis mRNA showed no significant difference (p≥0.05) between lamb quality traits. Conclusion: The DDC gene could be used as a potential candidate gene to improve lamb quality.

• Journal of Crop Science and Biotechnology
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• v.10 no.2
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• pp.98-105
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• 2007

Phylogenetic relationships in Korean watermelons were evaluated by genetic similarity coefficients using 15 SSR(simple sequence repeat), 14 SCAR(sequence characterized amplified region) and 14 CAPS(sequence characterized amplified region) markers. The SSR markers were selected from previously reported melon and watermelon SSRs through testing polymorphisms within a set of commercial $F_1$ varieties. The SCAR and CAPS markers were developed from polymorphic AFLP(amplified fragment length polymorphism) markers between inbred lines 'BN4001' and 'BN4002'. From the AFLP analysis, 105 polymorphic fragments were identified between the inbred lines using 1,440 primer combinations of EcoRI+CNNN and XbaI+ANNN. Based on the sequencing data of these polymorphic fragments, we synthesized sequence specific primer pairs and detected clear and reliable polymorphisms in 27 primer pairs by indels(insertion/deletion) or RFLP(restriction fragment length polymorphism). A total of 43 sequence-based PCR markers were obtained and polymorphic information content(PIC) was analyzed to measure the informativeness of each marker in watermelon varieties. The average PIC value of SCAR markers was 0.41, which was similar to that of SSR markers. Genetic diversity was also estimated by using these markers to assess the phylogenetic relationships among commercial varieties of watermelon. These markers differentiated 26 Korean watermelon varieties into two major phylogenetic groups, but this grouping was not significantly correlated with their morphological and physiological characteristics. The mean genetic similarity was 66% within the complete set of 26 commercial varieties. In addition, these sequence-based PCR markers were reliable and useful to identify cultivars and genotypes of watermelon.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.8
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• pp.1095-1099
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• 2006

Leptin and IGFBP-3 are two proteins that play an important role in growth and metabolism of the animals. They are also involved in the immune function of animals and, thus, are candidate genes for the study of association with immune functions. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) of these two genes was done to screen 64 crossbred (Holstein Friesian${\times}$Hariana) female calves of one year of age. From each RFLPs (fragments) three genotypes were observed. In all the RFLPs the mutant homozygotes were very less in numbers and, hence, were excluded from the least squares analysis. The serum IgG level was estimated using SRID assay. The mean level of serum IgG was $28.83{\pm}2.73mg/ml$. The effect of these identified genotypes on serum IgG level of calves at one year of age was analysed using least squares analysis. The HaeIII RFLP-AB genotype had significantly (p<0.05) higher serum IgG level ($31.86{\pm}3.05$) than the HaeIII RFLP-AA ($25.62{\pm}2.96$) genotype. There was no significant effect of leptin genotypes on the IgG level. The present results indicated a role of the IGFBP-3 gene on serum IgG level of cattle calves.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.9
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• pp.1145-1151
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• 2010

The objective of this work was to analyze the relationship between ovine major histocompatibility complex (MHC) DRB1 gene polymorphism and genetic resistance to hydatidosis in Kazakh sheep. The Ovar (ovine MHC) class II DRB1 second exon was amplified by polymerase chain reaction (PCR) from DNA samples of 702 Kazakh sheep, including 302 sheep with hydatidosis and 400 health controls. PCR products were characterized by the restriction fragment length polymorphism (RFLP) technique using five restriction enzymes, i.e., MvaI, HaeIII, SacI, SacII and Hin1I, yielding 14 alleles and 28 genotypes. Comparing the frequency of genotypes in hydatidosis sheep with the control group, it was found that the genotype frequencies of MvaIbc, Hin1Iab, SacIIab, HaeIIIde, HaeIIIdf and HaeIIIdd in control sheep were significantly (p<0.01) higher than in hydatidosis sheep, indicating that a significant correlation existed between these genotypes and resistance to hydatidosis. Genotype frequencies of MvaIbb, SacIIaa, Hin1Ibb and HaeIIIef in sheep with hydatidosis were extremely significantly (p<0.01) higher than in the control group, and the genotype frequency of HaeIIIab was significantly higher (p<0.05), indicating that a marked correlation existed between these genotypes and susceptibility to hydatidosis. By way of analyzing haplotype with these resistant genotypes, the hydatidosis resistant haplotype MvaIbc-SacIIab-Hin1Iab of Kazakh sheep was screened out, and then verified through artificial hydatid infection in sheep. The results indicated that the infection rate of sheep with the resistant haplotype of hydatidosis was significantly lower (p<0.01) than without this resistant haplotype. It showed that the genic haplotype MvaIbc-SacIIab-Hin1Iab of Ovar-DRB1 exon 2 was the resistant haplotype of hydatidosis in Kazakh sheep.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.5
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• pp.622-626
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• 2007

Using multi-trait animal model BLUP, selection was conducted over seven generations for growth rate (DG), real-time ultrasound loin-eye muscle area (LEA), backfat thickness (BF), and intramuscular fat content (IMF) to develop a new line of purebred Duroc pigs with enhanced meat production and meat quality. This study was intended to investigate the relationship between restriction fragment length polymorphism (RFLP) of a heart fatty acid-binding protein (H-FABP) gene and intramuscular fat content (IMF) of this Duroc purebred population. The present experiment examined the RFLP of 499 slaughtered pigs. The DNA was separated from the blood or ear tissue of the pigs, which were slaughtered at 105 kg of body weight. Intramuscular fat content of the longissimus muscle was measured using chemical analysis. A significant difference was detected in the breeding value of IMF among the H-FABP PCR RFLP genotypes. The AA genotype has a significantly larger positive effect on the IMF breeding value than do the Aa and aa genotypes for the MspI RFLP. In addition, the DD genotype has a significantly greater positive effect on IMF breeding value than the Dd and dd genotypes for the HaeIII RFLP. For the HinfI RFLP, the hh genotype has a significantly larger positive effect on IMF breeding value than the HH genotype. Multiple regression analysis was performed using the IMF breeding values as the dependent variable and the three H-FABP genotypes as independent variables. Results revealed that the contribution of the genotypes to variation in IMF breeding values was approximately 40%. These results demonstrated that H-FABP RFLPs affect IMF in this Duroc population.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.2
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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.

• Molecular Medicine Reports
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• v.21 no.4
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• pp.1973-1983
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• 2020

Silent brain infarction (SBI) is a cerebral infarction identified through brain imaging. In particular, studies have shown that the presence of SBI in elderly patients increases their risk of cognitive dysfunction, impairment and dementia. However, little research has been published on the relevance of SBI to these risks for the Korean population. The association between potassium voltage-gated channel subfamily Q member 2 (KCNQ2), transcription factor 4 (TCF4) and regulator of G-protein signaling 18 (RGS18) genotypes and SBI were investigated using whole-exome sequencing and PCR restriction fragment length polymorphism (RFLP) analysis. The study population included 407 patients with SBI (171 males) and 401 control subjects (172 males). Genotyping was performed using PCR RFLP. Interestingly, TCF4 rs9957668T>C polymorphisms were associated with SBI prevalence [TT vs. CC: adjusted odds ratio (AOR), 1.815, 95% confidence intervals (CI), 1.202-2.740; TT vs. TC+CC: AOR, 1.492, 95% CI, 1.066-2.088; TT+TC vs. CC: AOR, 1.454, 95% CI, 1.045-2.203]. The combination of KCNQ2 rs73146513A>G and TCF4 rs9957668T>C genotypes was associated with increasing SBI prevalence (AG/CC: AOR, 3.719, 95% CI, 1.766-7.833; AA/CC: AOR, 3.201, 95% CI, 1.387-7.387). The present study showed that TCF4 rs9957668T>C polymorphisms may be risk factors for SBI. Therefore, the TCF4 rs9957668T>C polymorphism may serve as a biomarker for increased risk of SBI in the Korean population.

• The Plant Pathology Journal
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• v.26 no.3
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• pp.223-230
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• 2010

The Burkholderia cepacia complex isolates causing bacterial fruit rot of apricot were characterized by speciesspecific PCR tests, recA-HaeIII restriction fragment length polymorphism (RFLP) assays, rep-PCR genomic fingerprinting, recA gene sequencing, and multilocus sequence typing (MLST) analysis. Results indicated that the isolates Bca 0901 and Bca 0902 gave positive amplifications with primers specific for B. vietnamiensis while the two bacterial isolates showed different recA-RFLP and rep-PCR profiles from those of B. vietnamiensis strains. In addition, the two bacterial isolates had a higher proteolytic activity compared with that of the non-pathogenic B. vietnamiensis strains while no cblA and esmR marker genes were detected for the two bacterial isolates and B. vietnamiensis strains. The two bacterial isolates were identified as Burkholderia seminalis based on recA gene sequence analysis and MLST analysis. Overall, this is the first characterization of B. seminalis that cause bacterial fruit rot of apricot.

• Clinical and Experimental Pediatrics
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• v.53 no.3
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• pp.432-436
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• 2010

Transient neonatal diabetes mellitus (TNDM) has been associated with paternal uniparental isodisomy of chromosome 6, paternally inherited duplication of 6q24, or a methylation defect at a CpG island of the ZAC or HYMAI gene. We experienced a case of TNDM in which the patient presented with hyperglycemia, macroglossia, and intrauterine growth retardation, caused by a paternally derived HYMAI. An 18-day-old female infant was admitted to the hospital because of macroglossia and recurrent hyperglycemia. In addition to the macroglossia, she also presented with large fontanelles, micrognathia, and prominent eyes. Serum glucose levels were 200-00 mg/dL and they improved spontaneously 2 days after admission. To identify the presence of a maternal methylated allele, bisulfite-treated genomic DNA from peripheral blood was prepared and digested with BssHII after polymerase chain reaction (PCR) amplification with methylation-specific HYMAI primers. PCR and restriction fragment length polymorphism analysis showed that the patient had only the paternal origin of the HYMA1 gene. TNDM is associated with a methylation defect in chromosome 6, suggesting that an imprinted gene on chromosome 6 is responsible for this phenotype.