• Asian-Australasian Journal of Animal Sciences
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• v.24 no.7
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• pp.889-897
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• 2011

Mycoplasma Pneumonia of swine (MPS) decreases the daily growth of pigs, and, co-infection with a virus sometimes causes severe pneumonia. Genetic selection of pigs resistant to the pulmonary MPS lesion might solve the economic loss due to MPS in animal production. Here, we examined the immunophenotype of Landrace line (Miyagino L2), genetically selected to reduce the incidence of pulmonary MPS lesion for 5 generations in Miyagi Prefecture Animal Industry Experiment Station. Although this line is expected to be resistant to the pulmonary MPS lesion, the biological characteristics of its immune function are not clear. We investigated details of the immunorelated phenotype of Miyagino L2 at the hematological and molecular biological level, including cytokine expression, and compared the results with that of non-genetically selected Landrace. Miyagino L2 showed decreased antigen-specific IgG and IgM production and increased CD8-positive T-cell population, and high levels of cortisol concentration, suggesting that the MPS-resistant phenotype is associated these immunological differences. Additionally, T-cell CD4 expression was highly correlated with the MPS expected breeding value. Although the detailed mechanisms underlying this high correlation remain unknown, our result suggested that the genetic selection of the expression level of CD4 might be useful to improve MPS resistance in pig production.

• Plant Biotechnology Reports
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• v.4 no.3
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• pp.201-211
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• 2010

We present a highly effective T-DNA inserted gene screening method as part of a reverse genetics model system using the Chinese cabbage (Brassica rapa L. spp. pekinensis). Three-step two-dimensional (2D) matrix strategies are potentially accurate and useful for the identification of specific T-DNA inserted mutants from a large population. To construct our Chinese cabbage model, we utilized a forward genetics screening approach for the abnormal phenotypes that were obtained from transgenic plants of Brassica rapa generated with Agrobacteria tumefaciens containing the pRCV2 vector. From one transgenic plant with an abnormal phenotype, we observed that the st1 gene (which is related to senescence-associated process proteins) contained a T-DNA fragment, and that its expression level was decreased. This T-DNA insert was then used as a control to construct an effective screening pool. As a result, the optimum template concentration was found to be 0.1-1 ng in our PCR strategy. For other conditions, positive changes to the Gibbs free energy prevented the formation of oligo dimers and hairpin loop structures, and autosegment extension gave better results for long fragment amplification. Using this effective reverse genetics screening method, only 23 PCR reactions were necessary to select a target gene from a pool of 100 individual DNAs. Finally, we also confirmed that the sequence we obtained from the above method was identical to the flanking sequence isolated by rescue cloning.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.10
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• pp.4319-4323
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• 2014

Background: Phospholipase C epsilon 1 (PLCE1) encodes a member of the phospholipase family of proteins that play crucial roles in carcinogenesis and progression of several cancers including esophageal cancer (EC). In two large scale genome-wide association studies (GWAS) single nucleotide polymorphisms (SNP, rs2274223A>G, rs3765524C>T) in PLCE1 were identified as novel susceptibility loci of esophageal cancer (EC) in China. The aim of the present study was to investigate this finding in Kashmir Valley, a high risk area. Materials and Methods: We determined genotypes of three potentially functional SNPs (rs2274223A>G, rs3765524C>T and rs7922612C>T) of PLCE1 in 135 EC patients, and 195 age and gender matched controls in Kashmiri valley by PCR RFLP method. Risk for developing EC was estimated by binary logistic regression using SPSS. Results: The selected PLCE1 polymorphisms did not show independent association with EC. However, the $G_{2274223}T_{3765524}T_{7922612}$ haplotype was significantly associated with increased risk of EC (OR=2.92; 95% CI=1.30-6.54; p=0.009). Smoking and salted tea proved to be independent risk factors for EC. Conclusions: Genetic variations in PLCE1 modulate risk of EC in the high risk Kashmiri population.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.10
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• pp.1369-1378
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• 2006

This is the first study in which genetic variability and relationships of a large number of Japanese chicken breeds were revealed along with those of several foreign breeds by using microsatellite DNA polymorphisms. Twenty-eight breeds (34 populations) of native Japanese chickens and seven foreign breeds or varieties were analyzed. The mean number of alleles per locus, the proportion of the polymorphic loci, and the expected average heterozygosity ranged from 1.75 to 4.70, from 0.55 to 1.00, and from 0.21 to 0.67, respectively. Microsatellite alleles being unique to a particular population were detected in some populations. The $D_A$ genetic distance between populations was obtained from allele frequency for every pair of the populations to construct a neighbor-joining tree. According to the phylogenetic tree, excluding a few exceptions, native Japanese chicken breeds and foreign breeds were clearly separated from each other. Furthermore, the tree topology divided native Japanese chickens into four main classes, which was almost in accordance with the classification based on body morphology; that is, (1) Cochin type, (2) Malay type, (3) layer type, and (4) intermediate type between Malay and layer types. This is the first finding for native Japanese chickens.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.10
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• pp.1261-1267
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• 2010

Milk production traits are important economic traits for dairy cattle. The aim of the present study was to refine the position of previously detected quantitative trait loci (QTL) on bovine chromosome 6 affecting milk production traits in Chinese Holstein dairy cattle. A daughter design with 918 daughters from 8 elite sire families and 14 markers spanning the previously identified QTL region were used in the analysis. We employed a combined linkage and linkage disequilibrium analysis (LDLA) approach with two options for calculating the IBD probabilities, one was based on haplotypes of all 14 markers (named Method 1) and the other based on haplotypes with sliding windows of 5 markers (named Method 2). For milk fat yield, the two methods revealed a highly significant QTL located within a 6.5 cM interval (Method 1) and a 4.0 cM interval (Method 2), respectively. For milk protein yield, a highly significant QTL was detected within a 3.0 cM interval (Method 1) or a 2.5 cM interval (Method 2). These results confirmed the findings of our previous study and other studies, and greatly narrowed down the QTL positions.

• Clinical and Experimental Reproductive Medicine
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• v.47 no.1
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• pp.61-67
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• 2020

Objective: In this study, specimens from testicular biopsies of men with nonobstructive azoospermia (NOA) were used to investigate whether RNF8 gene could serve as a biomarker to predict the presence of sperm in these patients. Methods: Testicular biopsy specimens from 47 patients were classified according to the presence of sperm (positive vs. negative groups) and investigated for the expression of RNF8. The level of RNF8 gene expression in the testes was compared between these groups using reverse-transcription polymerase chain reaction. Results: The expression level of RNF8 was significantly higher in testicular samples from the positive group than in those from the negative group. Moreover, the area under the curve of RNF8 expression for the entire study population was 0.84, showing the discriminatory power of RNF8 expression in differentiating between the positive and negative groups of men with NOA. A receiver operating characteristic curve analysis showed that RNF8 expression had a sensitivity of 81% and a specificity of 84%, with a cutoff level of 1.76. Conclusion: This study points out a significant association between the expression of RNF8 and the presence of sperm in NOA patients, which suggests that quantified RNF8 expression in testicular biopsy samples may be a valuable biomarker for predicting the presence of spermatozoa in biopsy samples.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.7
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• pp.930-938
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• 2019

Objective: Estimate genetic parameters, the rate of inbreeding, and the effect of inbreeding on growth and egg production traits of a Thai native chicken breed Lueng Hang Kao Kabinburi housed under intensive management under a tropical climate. Methods: Genetic parameters were estimated for weight measured at four weekly intervals from body weight at day 1 (BW1D) to body weight at 24 weeks (BW24) of age, as well as weight at first egg, age at first egg (AFE), egg weight at first egg, and total number of eggs (EN) produced during the first 17 weeks of lay using restricted maximum likelihood. Inbreeding depression was estimated using a linear regression of individual phenotype on inbreeding coefficient. Results: Direct additive genetic effect was significant for all traits. Maternal genetic effect and permanent environmental hen effects were significant for all early growth traits, expect for BW24. For BW24, maternal genetic effect was also significant. Permanent environmental hen effect was significant for AFE. Direct heritabilities ranged from 0.10 to 0.47 for growth traits and ranged from 0.15 to 0.16 for egg production traits. Early growth traits had high genetic correlations between them. The EN was lowly negatively correlated with other traits. The average rate of inbreeding for the population was 0.09% per year. Overall, the inbreeding had no effect on body weight traits, except for BW1D. An increase in inbreeding coefficient by 1% reduced BWID by 0.09 g (0.29% of the mean). Conclusion: Improvement in body weight gain can be achieved by selecting for early growth traits. Selection for higher body weight traits is expected to increase the weight of first egg. Due to low but unfavorable correlations with body weight traits, selection on EN needs to be combined with other traits via multi-trait index selection to improve body weight and EN simultaneously.

• Animal Bioscience
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• v.35 no.9
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• pp.1314-1326
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• 2022

Objective: Alongside the rise of animal-protection awareness in Taiwan, the public has been paying more attention to dog genetic deficiencies due to inbreeding in the pet market. The goal of this study was to isolate novel microsatellite markers for monitoring the genetic structure of domestic dog populations in Taiwan. Methods: A total of 113 DNA samples from three dog breeds-beagles (BEs), bichons (BIs), and schnauzers (SCs)-were used in subsequent polymorphic tests applying the 14 novel microsatellite markers that were isolated in this study. Results: The results showed that the high level of genetic diversity observed in these novel microsatellite markers provided strong discriminatory power. The estimated probability of identity (P_(ID)) and the probability of identity among sibs (P_(ID)sib) for the 14 novel microsatellite markers were 1.7×10^-12 and 1.6×10^-5, respectively. Furthermore, the power of exclusion for the 14 novel microsatellite markers was 99.98%. The neighbor-joining trees constructed among the three breeds indicated that the 14 sets of novel microsatellite markers were sufficient to correctly cluster the BEs, BIs, and SCs. The principal coordinate analysis plot showed that the dogs could be accurately separated by these 14 loci based on different breeds; moreover, the Beagles from different sources were also distinguished. The first, the second, and the third principal coordinates could be used to explain 44.15%, 26.35%, and 19.97% of the genetic variation. Conclusion: The results of this study could enable powerful monitoring of the genetic structure of domestic dog populations in Taiwan.

• The Korean Journal of Physiology and Pharmacology
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• v.17 no.6
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• pp.479-484
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• 2013

Given the CYP3A4 and CYP3A5's impact on the efficacy of drugs, the genetic backgrounds of individuals and populations are regarded as an important factor to be considered in the prescription of personalized medicine. However, genetic studies with Korean population are relatively scarce compared to those with other populations. In this study, we aimed to identify CYP3A4/5 polymorphisms and compare the genotype distributions among five ethnicities. To identify CYP3A4/5 SNPs, we first performed direct sequencing with 288 DNA samples which consisted of 96 Koreans, 48 European-Americans, 48 African-Americans, 48 Han Chinese, and 48 Japanese. The direct sequencing identified 15 novel SNPs, as well as 42 known polymorphisms. We defined the genotype distributions, and compared the allele frequencies among five ethnicities. The results showed that minor allele frequencies of Korean population were similar with those of the Japanese and Han Chinese populations, whereas there were distinct differences from European-Americans or African-Americans. Among the pharmacogenetic markers, frequencies of $CYP3A4^*1B$ (rs2740574) and $CYP3A5^*3C$ (rs776742) in Asian groups were different from those in other populations. In addition, minor allele frequency of $CYP3A4^*18$ (rs28371759) was the highest in Korean population. Additional in silico analysis predicted that two novel non-synonymous SNPs in CYP3A5 (+27256C>T, P389S and +31546T>G, I488S) could alter protein structure. The frequency distributions of the identified polymorphisms in the present study may contribute to the expansion of pharmacogenetic knowledge.

• Molecules and Cells
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• v.24 no.3
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• pp.338-342
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• 2007

Spinocerebellar ataxias (SCAs) are caused by expansion of (CAG)n triplet repeats. These repeats occur as polymorphic forms in general population; however, beyond a threshold size they become pathogenic. The sizes and distributions of repeats at the SCA1, SCA2, SCA3, SCA7 and DRPLA loci were assessed by molecular analysis of 124 unrelated ataxia patients and 44 controls, and the association of larger normal (LN) alleles with disease prevalence was evaluated. Triplet repeat expansions in the disease range were detected in 8% (10/124) of the cases, with the majority having expansion at the SCA1 locus. Normal allele ranges in the cohort studied were similar to the Caucasian and North Indian populations but differed from the Korean and Japanese populations at various loci. The percentage of individuals with LN alleles at the SCA1 and SCA2 loci was higher than reported in Indians, Japanese and Caucasians. LN alleles showed a good correlation with the incidence of SCA1, indicating that SCA1 is the most prevalent ataxia in our population. The majority of cases with clinical symptoms of SCA could not be diagnosed by established CAG repeat criteria, suggesting that there may be an alternative basis for disease pathogenesis: (i) Repeats lower than the normal range may also result in abnormal phenotypes (ii) LN alleles at different loci in the same individual may contribute to symptoms (iii) Exogenous factors may play a role in triggering disease symptoms in individuals with LN alleles (iv) Triplet repeats may reach the disease range in the brain but not in the blood.