• The Korean Journal of Physiology and Pharmacology
• /
• 제7권2호
• /
• pp.73-77
• /
• 2003

The effects of nitric oxide on the vestibular function recovery following unilateral labyrinthectomy (UL) were studied. Sprague-Dawley male rats, treated with nitric oxide liberating agent sodium nitroprusside (SNP) and NOS inhibitor $N^G$-nitro-L-arginine methyl ester (L-NAME), were subjected to destruction of the unilateral vestibular apparatus, and then spontaneous nystagmus was observed in the rat. To explore the effects of nitric oxide on the neuronal excitability, whole cell patch clamp technique was applied on isolated medial vestibular nuclear neurons. The frequency of spontaneous nystagmus in SNP treated rats was lesser than that of spontaneous nystagmus in control animals. In contrast, pre-UL treatment with L-NAME resulted in a significant increase in spontaneous nystagmus frequency. In addition, SNP increased the frequency of spontaneous action potential in isolated medial vestibular nuclear neurons. Potassium currents of the vestibular nuclear neurons were inhibited by SNP. After blockade of calcium dependent potassium currents by high EGTA (11 mM) in a pipette solution, SNP did not inhibit outward potassium currents. 1H-[1,2,4] oxadiazolo [4,3-a] quinozalin-1-one (ODQ), a specific inhibitor of soluble guanylyl cyclase, inhibited the effects of SNP on the spontaneous firing and the potassium current. These results suggest that nitric oxide after unilateral labyrinthectomy would help to facilitate vestibular compensation by inhibiting calcium-dependent potassium currents through increasing intracellular cGMP, and consequently would increase excitability in ipsilateral vestibular nuclear neurons.

• Asian-Australasian Journal of Animal Sciences
• /
• 제25권1호
• /
• pp.28-32
• /
• 2012

In the present study, we evaluated the informativeness of SNPs genotyped by the Illumina Bovine SNP50K assay in different cattle breeds. To investigate these on a genome-wide scale, we considered 52,678 SNPs spanning the whole autosomal and X chromosomes in cattle. Our study samples consists of six different cattle breeds. Across the breeds approximately 72 and 6% SNPs were found polymorphic and fixed or close to fix in all the breeds, respectively. The variations in the average minor allele frequency (MAF) were significantly different between the breeds studied. The level of average MAF observed in Hanwoo was significantly lower than the other breeds. Hanwoo breed also displayed the lowest number of polymorphic SNPs across all the chromosomes. More importantly, this study indicated that the Bovine SNP50K assay will have reduced power for genome-wide association studies in Hanwoo as compared to other cattle breeds. Overall, the Bovine SNP50K assay described in this study offer a useful genotyping platform for mapping quantitative trait loci (QTLs) in the cattle breeds. The assay data represent a vast and generally untapped resource to assist the investigation of the complex production traits and the development of marker-assisted selection programs.

• BMB Reports
• /
• 제40권1호
• /
• pp.95-99
• /
• 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
• /
• 제20권1호
• /
• pp.1-6
• /
• 2007

Leptin is the hormone product of the obese gene and is synthesized and secreted predominantly by white adipocytes and relates to the feedback system that regulates long-term body fat weight and composition. Therefore, the leptin gene could be an excellent candidate gene controlling fat deposition, carcass traits and meat quality in beef cattle. The objective of this study was to evaluate the association of 3 SNPs (A1127T and C1180T in exon 2 and C3100T in exon 3) in the bovine leptin gene with carcass and meat quality traits in Korean cattle. The C1180T SNP was associated with backfat thickness (BF) and marbling score (MS) (p<0.05). Animals with the genotype CC had higher BF than animals with TT genotype and higher MS compared with CT and TT genotypes. No significant associations were observed between the C3100T SNP and any carcass and meat quality traits analyzed. The effect of the A1127T SNP was not analyzed because the TT genotype was not detected and the AT genotype showed only 1.0% frequency. These results suggest that the C1180T SNP of the leptin gene may be useful as a genetic marker for carcass and meat quality traits in Korean cattle.

• 한국산학기술학회논문지
• /
• 제21권1호
• /
• pp.240-246
• /
• 2020

본 연구는 백우 품종 육성을 위해 분자생물학적 방법을 이용하여 유전적 특성을 파악하고 백우 품종을 식별하기 위한 백우 품종 특이적인 Single Nucleotide Polymorphism (SNP) 마커를 개발하기 위해 수행되었다. 한우 48두와 백우 22두의 혈액에서 추출된 DNA를 이용하여 Illumina Bovine HD 777K SNP chip으로 SNP genotyping을 실시하였다. 각 SNP의 Minor Allele Frequency (MAF) difference (한우와 백우의 차이 절대값)을 계산하고, Fisher's Exact test (Genotype)을 통해 MAF difference의 통계적 유의성(P-value)을 계산하였다. 품종 별 차이를 나타낼 수 있는 마커를 선발기준으로 MAF difference가 100%의 차이를 나타내는 SNP를 식별하였다. 이러한 유전적 차이를 보이는 9개의 단일염기다형성 마커(rs42125585, rs42125591, rs42125833, rs109461720, rs134735704, rs109447299, rs42164846, rs42160000 및 rs137353829)가 선발되었다. 선발된 마커들은 한우와 백우 특이적인 대립유전자를 가지고 서로 다른 대립유전자를 나타내고 있다. 이들 9개의 SNP 마커들을 이용하여 한우와 백우의 품종을 식별할 수 있음을 확인하였고, 이러한 결과들을 바탕으로 백우 품종 식별 마커 특허를 등록하였다. 백우는 원종인 한우에서 분리되어 한국재래종의 특성을 잘 나타내 주는 계통으로, 이러한 백우가 가지고 있는 유전적 특성 연구는 백우를 식별하고 품종으로서 육종하는데 사용되어 종축으로서의 가치 증진을 위한 기반 연구가 될 것으로 생각된다.

• Asian-Australasian Journal of Animal Sciences
• /
• 제23권12호
• /
• pp.1543-1551
• /
• 2010

A major aim of cattle genome research is to identify candidate genes associated with meat quantity and quality through QTL analysis for application in the livestock industry. Therefore, this study focused on discovery of useful SNPs within the LOC534614 gene, containing 12273_165 SNP which is located on the same site as the QTL on chromosome 6, and evaluation of the association between SNP and body weight and cold carcass weight in Hanwoo (Korean cattle) As a result of a BLAST search of the NCBI web site, we discovered that the mRNA sequence of the LOC534614 gene was similar to that of the coiled-coil domain containing 158 (CCDC158) for dog and human. According to the direct DNA sequence from the CCDC158 gene, we identified 19 polymorphic SNPs within exons and their flanking regions. Among them, 17 polymorphic SNPs were selected for genotyping in Hanwoo (n = 476) and seventeen marker haplotypes containing 12273_165 SNP (frequency >0.1) were identified. As a result of the association between 17 polymorphic SNPs and Hanwoo (n = 476), g.8778G>A SNP in exon 6 was found to be a non-synonymous SNP, and was significantly associated with body weight and cold carcass weight (p<0.05). We discovered 19 polymorphic SNPs in the CCDC158 gene on the QTL region of BTA 6 in Hanwoo and identified that the g.8778G>A SNP was significantly associated with body weight and cold carcass weight (p<0.05), which causes an amino acid variation from valine to methionine. Furthermore, statistical analysis demonstrated that the CCDC158 gene is strongly associated with body weight and cold carcass weight in Hanwoo. In this regard, the g.8778G>A SNP in the CCDC158 gene can be useful as a positional candidate for body weight and cold carcass weight for marker-assisted selection in Hanwoo.

• Genomics & Informatics
• /
• 제10권3호
• /
• pp.200-205
• /
• 2012

Although a large number of single nucleotide polymorphisms (SNPs) have been identified from the bovine genome-sequencing project, few of these have been validated at large in Bos indicus breeds. We have genotyped 192 animals, representing 5 cattle populations of Ethiopia, with the Illumina Bovine 8K SNP BeadChip. These include 1 Sanga (Danakil), 3 zebu (Borana, Arsi and Ambo), and 1 zebu ${\times}$ Sanga intermediate (Horro) breeds. The Hanwoo (Bos taurus) was included for comparison purposes. Analysis of 7,045 SNP markers revealed that the mean minor allele frequency (MAF) was 0.23, 0.22, 0.21, 0.21, 0.23, and 0.29 for Ambo, Arsi, Borana, Danakil, Horro, and Hanwoo, respectively. Significant differences of MAF were observed between the indigenous Ethiopian cattle populations and Hanwoo breed (p < 0.001). Across the Ethiopian cattle populations, a common variant MAF (${\geq}0.10$ and ${\leq}0.5$) accounted for an overall estimated 73.79% of the 7,045 SNPs. The Hanwoo displayed a higher proportion of common variant SNPs (90%). Investigation within Ethiopian cattle populations showed that on average, 16.64% of the markers were monomorphic, but in the Hanwoo breed, only 6% of the markers were monomorphic. Across the sampled Ethiopian cattle populations, the mean observed and expected heterozygosities were 0.314 and 0.313, respectively. The level of SNP variation identified in this particular study highlights that these markers can be potentially used for genetic studies in African cattle breeds.

• BMB Reports
• /
• 제41권4호
• /
• pp.334-337
• /
• 2008

MCL1 expression has been found to be up-regulated during infection with virulent Mycobacterium tuberculosis. We investigated the genetic polymorphisms in MCL1 as potential candidate gene for a host genetic study of clinical TB infection. We have sequenced exons and their boundaries of MCL1, including the 1.5 kb promoter region, to identify polymorphisms, and eight polymorphisms were identified. The genetic associations of polymorphisms in MCL1 with clinical TB patients (n=486) and normal controls (n=370) were analyzed. Using statistical analyses, one common promoter polymorphism (MCL1-324C>A) which is absolutely linked with three other SNPs in the promoter and 3'UTR regions, were found to be significantly associated with increased risk of clinical TB disease. The frequency of the A-bearing genotype of -324C>A was higher in clinical TB patients than in normal controls (P=0.0008, OR=1.68). Our findings suggest that polymorphisms in MCL1 might be one of genetic factors for the risk of clinical tuberculosis development.

• Genomics & Informatics
• /
• 제9권4호
• /
• pp.181-188
• /
• 2011

In planning a model-based phylogenic study for highly related ethnic data, the SNP marker number is an important factor to determine for relationship inferences. Genotype frequency data, utilizing a sub sampling method, from 63 Pan Asian ethnic groups was used for determining the minimum SNP number required to establish such relationships. Bootstrap random sub-samplings were done from 5.6K PASNPi SNP data. DA distance was calculated and neighbour-joining trees were drawn with every re-sampling data set. Consensus trees were made with the same 100 sub-samples and bootstrap proportions were calculated. The tree consistency to the one obtained from the whole marker set, improved with increasing marker numbers. The bootstrap proportions became reliable when more than 7,000 SNPs were used at a time. Within highly related ethnic groups, the minimum SNPs number for a robust neighbor-joining tree inference was about 7,000 for a 95% bootstrap support.

• Journal of Animal Science and Technology
• /
• 제49권6호
• /
• pp.719-728
• /
• 2007

CSRP3, APOBEC2, CAV1, CAV2 및 CAV3 유전자들은 포유동물에서 도체와 육질 형질에 중요한 역할을 하는 것으로 보고되고 있다. 따라서, 이 유전자들의 단일염기다형(Single nucleotide poly- morphism; SNP)을 8개의 다른 소의 품종에서 확인한 결과 coding region에서 caveolin family 유전자에서 9개의 SNP, CSRP3유전자에서 1개의 SNP 및 APOBEC2 유전자에서 3개의 SNP가 존재함을 확인하였다. 이 coding region의 SNP들은 PCR-RFLP 방법에 의해 재확인하였으며 이들 유전자의 intronic region에서도 9개의 SNP가 존재함을 확인할 수 있었다. 8개의 다른 품종 소에 각 유전자들의 SNP들을 이용하여 유전자 빈도를 확인한 결과 CAV2, CAV3, CSRP3 및 APOBEC2 유전자의 SNP 중에서 5개가 품종간에서 유의적으로 차이가 있음을 확인할 수 있었다. 이 SNP들은 차후 검증작업을 통하여 육질관련 형질 마커로 이용될 수 있을 것으로 사료된다.