• Asian-Australasian Journal of Animal Sciences
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• v.33 no.11
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• pp.1725-1731
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• 2020

Objective: An initial RNA-Sequencing study revealed that UDP-galactose-4-epimerase (GALE) was one of the most promising candidates for milk protein concentration in Chinese Holstein cattle. This enzyme catalyzes the interconversion of UDP-galactose and UDP-glucose, an important step in galactose catabolism. To further validate the genetic effect of GALE on milk protein traits, genetic variations were identified, and genotypes-phenotypes associations were performed. Methods: The entire coding region and the 5'-regulatory region (5'-UTR) of GALE were re-sequenced using pooled DNA of 17 unrelated sires. Association studies for five milk production traits were performed using a mixed linear animal model with a population encompassing 1,027 Chinese Holstein cows. Results: A total of three variants in GALE were identified, including two novel variants (g.2114 A>G and g.2037 G>A) in the 5'-UTR and one previously reported variant (g.3836 G>C) in an intron. All three single nucleotide polymorphisms (SNPs) were associated with milk yield (p<0.0001), fat yield (p = 0.0006 to <0.0001), protein yield (p = 0.0232 to <0.0001) and protein percentage (p<0.0001), while no significant associations were detected between the SNPs and fat percentage. A strong linkage disequilibrium (D' = 0.96 to 1.00) was observed among all three SNPs, and a 5 Kb haplotype block involving three main haplotypes with GAG, AGC, and AGG was formed. The results of haplotype association analyses were consistent with the results of single locus association analysis (p<0.0001). The phenotypic variance ratio above 3.00% was observed for milk protein yield that was explained by SNP-g.3836G >C. Conclusion: Overall, our findings provided new insights into the polymorphic variations in bovine GALE gene and their associations with milk protein concentration. The data indicate their potential uses for marker-assisted breeding or genetic selection schemes.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.7
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• pp.942-948
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• 2005

New polymorphism of major histocompatibility complex B-G genes was investigated by amplification and digestion of a 401bp fragment including intron 1 and exon 2 using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique with two restriction enzymes of Msp I and Tas I in eight breeds of Chinese indigenous chickens and one exotic breed. In the fragment region of the gene, three novel single nucleotide polymorphisms (SNPs) were detected at the two restriction sites. We found the transition of two nucleotides of A294G and T295C occurred at Tas I restriction site, and consequently led to a non-synonymous substitution of asparagine into serine at position 54 within the deduced amino acid sequence of immunoglobulin variable-region-like domain encoded by the exon 2 of B-G gene. It was observed at rare frequency that a single mutation of A294G occurring at the site, also caused an identical substitution of amino acid, asparagine 54-to-serine, to that we described previously. And the transversion of G319C at Msp I site led to a non-synonymous substitution, glutamine 62-to-histidine. The new alleles and allele frequencies identified by the PCR-RFLP method with the two enzymes were characterized, of which the allele A and B frequencies at Msp I and Tas I loci were given disequilibrium distribution either in the eight Chinese local breeds or in the exotic breed. By comparison, allele A at Msp I locus tended to be dominant, while, the allele B at Tas I locus tended to be dominant in all of the breeds analyzed. In Tibetan chickens, the preliminary association analysis revealed that no significant difference was observed between the different genotypes identified at the Msp I and Tas I loci and the laying performance traits, respectively.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.11
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• pp.1544-1550
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• 2008

The retinoids (vitamin A and its derivatives) play a critical role in vision, growth, reproduction, cell differentiation and embryonic development. Using the IMpRH panel, porcine cellular retinol binding protein genes 5 and 7 (RBP5 and RBP7) were assigned to porcine chromosomes 5 and 6, respectively. The complete coding sequences (CDS) of the RBP5 and RBP7 genes were amplified using the reverse transcriptase polymerase chain reaction (RT-PCR) method, and the deduced amino acid sequences of both genes were compared to human corresponding proteins. The mRNA distributions of the two genes in adult Wuzhishan pig tissues (lung, skeletal muscle, spleen, heart, stomach, large intestine, lymph node, small intestine, liver, brain, kidney and fat) were examined. A total of nine single nucleotide polymorphisms (SNPs) were identified in two genes. Three of these SNPs were analyzed using the polymerase chain reaction-restriction-fragment length polymorphism (PCR-RFLP) method in Laiwu, Wuzhishan, Guizhou, Bama, Tongcheng, Yorkshire and Landrace pig breeds. Association analysis of genotypes of these SNP loci with economic traits was done in our experimental populations. Significant associations of different genotypes of $RBP5-A/G^{63}$, $RBP5-A/G^{517}$ and $RPB5-T/C^{intron1-90}$ loci with traits including maximum carcass length (LM), minimum carcass length (LN), marbling score (MS), back fat thickness at shoulder (SBF), meat color score (MCS) and hematocrit (HCT) were detected. These SNPs may be useful as genetic markers in genetic improvement for porcine production.

• Journal of Plant Biotechnology
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• v.29 no.2
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• pp.85-92
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• 2002

This study has been focused on improving transformation efficiency of rice using Agrobacterium tumefaciens. We have demonstrated the effect of this system when the GPAT gene related to the cold-resistance was transferred by Agrobacterium tumefaciens in rice. Transformation conditions were modified using intron $\beta$-glucuronidase (GUS) expression as a reporter gene in the rice. In this study, mature seed-derived calli of rice (Oruza sativa L. cv. Dongjin) were pre-cultured for 3 days and then infected with Agrobacterium. When this infected calli were cultured in the dark for 10 days on co-cu]lure medium containing 50 mg/L of CaCl$_2$, 30 mg/L of acetosyringone, 2 mg/L of 2,4-D, 120 mg/L of betaine, high GUS expression was observed. In the present transformation system, the efficiency of transformation of GPAT gene was about 54%. Stable integration of GPAT gene into chromosomal DNA was proven by southern blot analysis of genomic DNA isolated from T$_{0}$ progenies. The progenies (T1 generation) derived from primary transformant of 5 lines were segregated with a 3 (resistant) : 1 (sensitive ratio) in medium containing hygromycin. This high frequency transformation system can be used as a useful tool in transformation of another monocotyledon.n.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.6 no.1
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• pp.15-23
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• 2006

Purpose: Glycogen storage disease type III (GSD-III), is a rare autosomal recessive disorder of glycogen metabolism. The affected enzyme is amylo-1,6-glucosidase, 4-alpha-glucanotransferase (AGL, glycogen debranching enzyme), which is responsible for the debranching of the glycogen molecule during catabolism. The disease has been demonstrated to show clinical and biochemical heterogeneity, reflecting the genotype-phenotype heterogeneity among different patients. In this study, we analyzed mutations of the AGL gene in three unrelated Korean GSD-III patients and discussed their clinical and laboratory implications. Methods: We studied three GSD-III patients and the clinical features were characterized. Sequence analysis of 35exons and part exon-intron boundaries of the AGLgene in patients were carried out by direct DNA sequencing method using genomic DNA isolated from patients' peripheral leukocytes. Results: The clinical features included hepatomegaly (in all patients), seizures (in patient 2), growth failure (in patients 1), hyperlipidemia (in patients 1 and 3), raised transaminases and creatinine kinase concentrations (in all patients) and mild EKG abnormalities (in patients 2). Liver transplantation was performed in patient 2due to progressive hepatic fibrosis. Administration of raw-corn-starch could maintain normoglycemia and improve the condition. DNA sequence analysis revealed mutations in 5 out of 6 alleles. Patient 1 was a compound heterozygote of c.1282 G>A (p.R428K) and c.1306delA (p.S603PfsX6), patient 2 with c.1510_1511insT (p.Y504LfsX10), and patient 3 with c.3416 T>C (p.L1139P) and c.l735+1 G>T (Y538_R578delfsX4) mutations. Except R428K mutation, 4 other mutations identified in3 patients were novel. Conclusion: GSD-III patients have variable phenotypic characteristics resembling GSD-Ia. The molecular defects in the AGL gene of Korean GSD-III patients were genetically heterogeneous.

• Journal of Animal Science and Technology
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• v.51 no.4
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• pp.289-294
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• 2009

Inositol 1,4,5-triphosphate receptor type 1 (IP3R1) is a $Ca^{2+}$ release channel that responds to the second messenger IP3 and that modulates diverse cellular functions such as contraction/excitation, secretion, gene expression and cellular growth. We discovered single nucleotide polymorphisms (SNPs) within IP3R1 gene and analyzed associations between gene polymorphisms and carcass traits in Korean cattle (Hanwoo) in order to develop novel DNA markers at genomic level. Three SNPs were detected at the position of g.1428617A>G, g.1418843C>T and g.1414377C>T with 24 unrelated Hanwoo samples by direct sequencing of the PCR products. We found that genotype of g.1414377C>T SNP was associated with live weight (P<0.05) and carcass weight (P<0.01) using the general linear model of SAS package. These results suggest that polymorphism of IP3R1 gene was associated with weight-related traits in Hanwoo.

• Journal of Life Science
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• v.27 no.7
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• pp.760-766
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• 2017

Genotypes of the nucleotide substitution g.23655332G>C of SNP marker rs385360448 at Lysophospholipase I (LYPLA1) gene intron 7, were tested for their effect on the carcass traits of Hanwoo and Jeju Crossbred cattle ($F_1$ progeny produced between Hanwoo ${\times}$ Jeju Black cattle) populations on Jeju Island. In the Hanwoo steer population, the meats containing LYPLA1 rs385360448 G/- genotypes showed significantly higher marbling scores and greater texture indices, compared to those of rs385360448 C/C homozygous animals (p<0.05). However, the LYPLA1 genotypes were not associated with the levels of carcass weight, backfat thickness, eye muscle area (EMA), meat color, and fat color (p>0.05). On the other hand, in the JCC steer population, the LYPLA1 G/- harboring meats showed significantly greater EMA levels, compared to those of C/C homozygotes (p<0.05). The results of the present study indicate that the LYPLA1 genotypes could alter the levels of intramuscular fat deposition, texture index, and eye muscle area via phospholipid metabolism in the Longissimus dorsi muscle of the cattle. These findings suggested that LYPLA1 genotypes may effect molecular genetic markers in the improvement of carcass traits of Hanwoo and Jeju Black industrial cattle populations on Jeju Island.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.35 no.5
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• pp.490-496
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• 2002

In order to detect the DNA heteropolymorphism of chum salmon, selected essential genes were examined in different regional chum salmons, i.e., Korean, Japanese and American by denaturing gradient gel electrophoresis (DGGE) and real time PCR methods. From the promoter regions and introns of growth hormone, mtDNA NDI region, D-loop region, IGF-I, histone H3 and MCH2 several representative primer pairs were obtained and employed for the DGGE with the PCR products from the genomic DNAs of the different regional chum salmons. mtDNA NDI, D-loop region and IGE-I genes showed marked heteropolymorphism between Korean and American chum salmons. Intron C of growth hormone also showed a heteropolymorphism between Korean and Japanese chum salmons. Whereas heteropolnnorphism of histone liH and MCH2 genes was detected among in Korean, Japanese and Asnerican chum salmons in the examined region. The real time PCR disclosed the characteristic incremental production of target DNAs dependent on the heteropolymorphic conditions of genomic DNAa of chum salmons, thus the different regional chum salmons could be grouped by the variable incremental curies. Although the DGGE and real time PCR did not produce the identical results in this study, we suggest that the DGGE and real time PCR could be used for the primary screening of the DNA heteropolymorphism of different animal genome.

• Molecules and Cells
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• v.38 no.11
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• pp.950-958
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• 2015

BCS1L gene encodes mitochondrial protein and is a member of conserved AAA protein family. This gene is involved in the incorporation of Rieske FeS and Qcr10p into complex III of respiratory chain. In our previous study, AluYRa2-derived alternative transcript in rhesus monkey genome was identified. However, this transcript has not been reported in human genome. In present study, we conducted evolutionary analysis of AluYRa2-exonized transcript with various primate genomic DNAs and cDNAs from humans, rhesus monkeys, and crabeating monkeys. Remarkably, our results show that AluYRa2 element has only been integrated into genomes of Macaca species. This Macaca lineage-specific integration of AluYRa2 element led to exonization event in the first intron region of BCS1L gene by producing a conserved 3' splice site. Intriguingly, in rhesus and crabeating monkeys, more diverse transcript variants by alternative splicing (AS) events, including exon skipping and different 5' splice sites from humans, were identified. Alignment of amino acid sequences revealed that AluYRa2-exonized transcript has short N-terminal peptides. Therefore, AS events play a major role in the generation of various transcripts and proteins during primate evolution. In particular, lineage-specific integration of Alu elements and species-specific Alu-derived exonization events could be important sources of gene diversification in primates.

• Journal of Genetic Medicine
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• v.8 no.1
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• pp.53-57
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• 2011

Purpose: Wilson disease is an autosomal recessive disorder which causes excessive copper accumulation in the hepatic region. So far, ATP7B gene is the only disease-causing gene of Wilson disease known to date. However, ATP7B mutations have not been found in ~15% of the patients. This study was performed to identify any causative gene in Wilson disease patients without an ATP7B mutation in either allele. Materials and Methods: The sequence of the coding regions and exon-intron boundaries of the five ATP7B-interacting genes, ATOX1, COMMD1, GLRX, DCTN4, and ZBTB16, were analyzed in the 12 patients with Wilson disease. Results: Three nonsynonymous variants including c.1084A>G (p.Thr362Ala) in the exon 12 of the DCTN4 gene were identified in the patients examined. Among these, only p.Thr362Ala was predicted as possibly damaging protein function by in silico analysis. Examination of allele frequency of c.1084A>G (p.Thr362Ala) variant in the 176 patients with Wilson disease and in the 414 normal subjects revealed that the variant was more prevalent in the Wilson disease patients (odds ratio [OR]=3.14, 95% confidence interval=1.36-7.22, P=0.0094). Conclusion: Our result suggests that c.1084A>G (p.Thr362Ala) in the ATP7B-interacting DCTN4 gene may be associated with the pathogenesis of Wilson disease.