• Asian Pacific Journal of Cancer Prevention
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• 제15권2호
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• pp.763-767
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• 2014

Aim: To study the contribution of genetic variation in RAD51 to risk of esophageal squamous cell carcinoma (ESCC). Methods: Three single nucleotide polymorphisms (SNPs) in RAD51 (rs1801320, rs4144242 and rs4417527) were genotyped in 316 ESCC patients and 316 healthy controls in Anyang area of China using PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism). Demographic variables between cases and controls were statistically compared by T test and Chi-square test. Hardy-Weinberg equilibrium was evaluated by the Chi-square test. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to measure any association with ESCC. Haplotype frequencies were estimated by Phase 2.1. Result: The genotype frequencies of rs1801320, rs4144242 and rs4417527 in patients with ESCC demonstrated no significant differences from those in control group (P>0.05). When the haplotypes of these three SNPs were constructed and their relationships with ESCC risk investigated, however, CGG was observed to increase the risk (P=0.020, OR=2.289). Conclusions: There was no association between the three SNPs of RAD51 and ESCC susceptibility in our Chinese population. However, the CGG haplotype might be a risk factor.

• Asian-Australasian Journal of Animal Sciences
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• 제29권2호
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• pp.170-175
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• 2016

The objective of this study was to assess variance components and genetic parameters for fat and protein content in Tsigai sheep using multivariate animal models in which fat and protein content in individual months of lactation were treated as different traits, and univariate models in which fat and protein content were treated as repeated measures of the same traits. Test day measurements were taken between the second and the seventh month of lactation. The fixed effects were lactation number, litter size and days in milk. The random effects were animal genetic effect and permanent environmental effect of ewe. The effect of flock-year-month of test day measurement was fitted either as a fixed (FYM) or random (fym) effect. Heritabilities for fat content were estimated between 0.06 and 0.17 (FYM fitted) and between 0.06 and 0.11 (fym fitted). Heritabilities for protein content were estimated between 0.15 and 0.23 (FYM fitted) and between 0.10 and 0.18 (fym fitted). For fat content, variance ratios of permanent environmental effect of ewe were estimated between 0.04 and 0.11 (FYM fitted) and between 0.02 and 0.06 (fym fitted). For protein content, variance ratios of permanent environmental effect of ewe were estimated between 0.13 and 0.20 (FYM fitted) and between 0.08 and 0.12 (fym fitted). The proportion of phenotypic variance explained by fym effect ranged from 0.39 to 0.43 for fat content and from 0.25 to 0.36 for protein content. Genetic correlations between individual months of lactation ranged from 0.74 to 0.99 (fat content) and from 0.64 to 0.99 (protein content). Fat content heritabilities estimated with univariate animal models roughly corresponded with heritability estimates from multivariate models: 0.13 (FYM fitted) and 0.07 (fym fitted). Protein content heritabilities estimated with univariate animal models also corresponded with heritability estimates from multivariate models: 0.18 (FYM fitted) and 0.13 (fym fitted).

• Asian-Australasian Journal of Animal Sciences
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• 제18권9호
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• pp.1209-1216
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• 2005

This study aimed to use field data collected by the Hokkaido Dairy Cattle Milk Recording and Testing programs to estimate genetic parameters for concentration of milk urea nitrogen (MUN) and predicted Digestive Crude Protein Percentage of requirement (DCPun). Edited data consisted of 5,797,500 test-day records of MUN and yields of milk, fat, and protein obtained from 783,271cows in Holstein herds in Hokkaido, Japan. Data were divided into four datasets; for the first, second, third and fourth lactations. Two analyses were performed on data from each lactation. First, ANOVA was used to estimate the significance of the effects of several environmental factors on MUN and DCPun, after absorbing the Herd-Test-Day (HTD) effects. The effects of DIM and age.season effects had significant impact on MUN and DCPun. The second used a multi-traits repeatability model (MTRM) to estimate heritabilities and genetic correlations of milk with MUN and DCPun. Heritability estimates for MUN and DCPun in the first, second, and third lactations were 0.21:0.16, 0.20:0.16, and 0.20:0.18, respectively. Genetic correlations for milk with MUN and DCPun in the first, second, and third lactations were 0.02 - 0.17, and -0.25 - -0.39, respectively. The results indicate that MUN and DCPun are possibly effective tools for improving the energy balance, but that the relationships between MUN and other economically important traits such as feed efficiency, metabolic disease and fertility are still necessary.

• Asian-Australasian Journal of Animal Sciences
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• 제19권1호
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• pp.13-18
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• 2006

Two different animal models, which differ in whether or not taking maternal genetic effect into account, for estimating genetic parameters of cashmere weight, live body weight, cashmere thickness, staple length, fiber diameter, and fiber length in Inner Mongolia White Cashmere Goat were compared via likelihood ratio test. The results indicate that maternal genetic effect has significant influence on live body weight and cashmere thickness, but no significant influence on the other traits. Using models suitable for each trait, both genetic parameters and trends were analyzed with the MTDFREML program. Heritability estimates from single trait models for cashmere weight, live body weight, cashmere thickness, staple length, fiber diameter and fiber length were found to be 0.30, 0.07, 0.21, 0.29, 0.28 and 0.21, respectively. Genetic correlation estimates from two-trait models between live body weight and all other traits (-0.06~0.07) was negligible, as were those between fiber diameter and all other traits (-0.01~0.03) except cashmere thickness (0.19). Cashmere weight and staple length had moderate to low genetic correlations with other traits (-0.24~0.39 and -0.24~0.34, respectively) except for live body weight and fiber diameter. Cashmere thickness had a strong genetic correlation with fiber length (0.81), and low genetic correlation with other traits (0.19~0.34) except live body weight. Genetic trend analysis suggests that selection for cashmere weight was very effective, which has led to the slow genetic progress of cashmere thickness and fiber length due to their genetic correlations with cashmere weight. The selection for live body weight was not effective, which was consistent with its low inheritability.

• Asian Pacific Journal of Cancer Prevention
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• 제16권7호
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• pp.2713-2717
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• 2015

Background: Possible associations between the single nucleotide polymorphism (SNP) rs8034191 in the aminoglycosidephosphotransferase domain containing 1 (AGPHD1) gene and lung cancer risk have been studied by many researchers but the results have been contradictory. Materials and Methods: A computerized search for publications on rs8034191 and lung cancer risk was performed. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess the association between rs8034191 and lung cancer risk with 13 selected case-control studies. Sensitivity analysis, test of heterogeneity, cumulative meta-analysis, and assessment of bias were also performed. Results: A significant association between rs8034191 and lung cancer susceptibility was found using the dominant genetic model (OR=1.344, 95% CI: 1.285-1.406), the additive genetic model (OR=1.613, 95% CI: 1.503-1.730), and the recessive genetic model (OR=1.408, 95% CI: 1.319-1.503). Moreover, an increased lung cancer risk was found with all genetic models after stratification of ethnicity. Conclusions: The association between rs8034191 and lung cancer risk was significant using multiple genetic models, suggesting that rs8034191 is a risk factor for lung cancer. Further functional studies of this polymorphism and lung cancer risk are warranted.

• Asian-Australasian Journal of Animal Sciences
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• 제31권6호
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• pp.804-811
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• 2018

Objective: Complete mtDNA D-loop sequences of four Thai indigenous chicken varieties, including Pra-dhu-hang-dam (PD), Leung-hang-khao (LK), Chee (CH), and Dang (DA) were explored for genetic diversity and relationships with their potential ancestor and possible associates to address chicken domestication in Thailand. Methods: A total of 220 complete mtDNA D-loop sequences of the four Thai indigenous chicken varieties were obtained by Sanger direct sequencing of polymerase chain reaction amplicons of 1,231 to 1,232 base pair in size. A neighbor-joining dendrogram was constructed with reference complete mtDNA D-loop sequences of Red Junglefowl (RJF) and those different chicken breeds available on National Center for Biotechnology Information database. Genetic diversity indices and neutrality test by Tajima's D test were performed. Genetic differences both within and among populations were estimated using analysis of molecular variance (AMOVA). Pairwise fixation index ($F_{ST}$) was conducted to evaluated genetic relationships between these varieties. Results: Twenty-three identified haplotypes were classified in six haplogroups (A-E and H) with the majority clustered in haplogroup A and B. Each variety was in multiple haplogroups with haplogroups A, B, D, and E being shared by all studied varieties. The averaged haplotype and nucleotide diversities were, respectively 0.8607 and 0.00579 with non-significant Tajima's D values being observed in all populations. Haplogroup distribution was closely related to that of RJF particularly Gallus gallus gallus (G. g. gallus) and G. g. spadiceus. As denoted by AMOVA, the mean diversity was mostly due to within-population variation (90.53%) while between-population variation (9.47%) accounted for much less. By pairwise $F_{ST}$, LK was most closely related to DA ($F_{ST}=0.00879$) while DA was farthest from CH ($F_{ST}=0.24882$). Conclusion: All 4 Thai indigenous chickens are in close relationship with their potential ancestor, the RJF. A contribution of shared, multiple maternal lineages was in the nature of these varieties, which have been domesticated under neutral selection.

• 대한영양사협회학술지
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• 제12권3호
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• pp.225-234
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• 2006

The purpose of this study was to identify the factors that related to obesity among 6th grade elementary school girls. The study subjects were 337 girls residing in Seoul. Not only variables of nutritional environment such as eating habits, health related behavioral variables, nutritional feeding methods during infancy, and genetic factors but also sexual maturity had been included as a obesity related factors. Association between obesity and related variables were analyzed by $x^2$(Chi-square) test. The obesity prevalence of the study subjects were 16% based on Röhrer Index(RI). Fifty-three percent of the study subjects experienced menarche at the time of data collection. Result of analysis showed that not only the nutritional enviromental variables such as eating habits, specific food preferences, and habit of exercise but also genetic factors did not show any statistically significant association with obesity. Above finding may imply that more variables other than the variables included in this study might have influenced on the obesity of the children. However sexual maturity in term of breast development showed significant association with obesity.

• Asian-Australasian Journal of Animal Sciences
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• 제21권6호
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• pp.776-783
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• 2008

In this study, we investigated the genetic diversity and phylogenetic relationship of six duck populations by employing the genetic polymorphisms of 20 microsatellites. The parameters used in this study included number of alleles, average effective numbers of alleles (E) and average rates of heterozygosity of each population. The results showed that all the microsatellite loci were highly polymorphic except that the locus AJ515896 in Muscovy duck was 0. The average PIC (0.762), average h (0.7843) and average E (5.261) of the six duck populations were all high, indicating that the gene polymorphisms and genetic diversity were high. The test of Hardy-Weinberg equilibrium showed that the six populations in this study were all in Hardy-Weinberg disequilibrium. The F-statistic analysis results showed the range of FST was from 0.0205 (AJ515895) to 0.2558 (AJ515896). The mean FST was 0.0936. Phylogenetic study revealed that Peking duck (Z1 and Z4), Shaoxing duck, Cherry Valley duck and Aobaixing duck were clustered in one group, while the Muscovy duck was clustered in one group alone. The phylogenetic relationships among different populations were in accordance with their breeding history and distribution. Our data suggested that the 20 microsatellite loci were effective markers for analysis of genetic relationships among duck populations.

• Asian-Australasian Journal of Animal Sciences
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• 제33권10호
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• pp.1558-1565
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• 2020

Objective: The objective of this study was to characterize the number of loci affecting growth traits and the distribution of single nucleotide polymorphism (SNP) effects on growth traits, and to understand the genetic architecture for growth traits in Hanwoo (Korean cattle) using genome-wide association study (GWAS), genomic partitioning, and hierarchical Bayesian mixture models. Methods: GWAS: A single-marker regression-based mixed model was used to test the association between SNPs and causal variants. A genotype relationship matrix was fitted as a random effect in this linear mixed model to correct the genetic structure of a sire family. Genomic restricted maximum likelihood and BayesR: A priori information included setting the fixed additive genetic variance to a pre-specified value; the first mixture component was set to zero, the second to 0.0001×σ²_g, the third 0.001×σ²_g, and the fourth to 0.01×σ²_g. BayesR fixed a priori information was not more than 1% of the genetic variance for each of the SNPs affecting the mixed distribution. Results: The GWAS revealed common genomic regions of 2 Mb on bovine chromosome 14 (BTA14) and 3 had a moderate effect that may contain causal variants for body weight at 6, 12, 18, and 24 months. This genomic region explained approximately 10% of the variance against total additive genetic variance and body weight heritability at 12, 18, and 24 months. BayesR identified the exact genomic region containing causal SNPs on BTA14, 3, and 22. However, the genetic variance explained by each chromosome or SNP was estimated to be very small compared to the total additive genetic variance. Causal SNPs for growth trait on BTA14 explained only 0.04% to 0.5% of the genetic variance Conclusion: Segregating mutations have a moderate effect on BTA14, 3, and 19; many other loci with small effects on growth traits at different ages were also identified.

• Genomics & Informatics
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• 제14권4호
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• pp.181-186
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• 2016

Glucose tolerance tests have been devised to determine the speed of blood glucose clearance. Diabetes is often tested with the standard oral glucose tolerance test (OGTT), along with fasting glucose level. However, no single test may be sufficient for the diagnosis, and the World Health Organization (WHO)/International Diabetes Federation (IDF) has suggested composite criteria. Accordingly, a single multi-class trait was constructed with three of the fasting phenotypes and 1- and 2-hour OGTT phenotypes from the Korean Association Resource (KARE) project, and the genetic association was investigated. All of the 18 possible combinations made out of the 3 sets of classification for the individual phenotypes were taken into our analysis. These were possible due to a method that was recently developed by us for estimating genomic associations using a generalized index of dissimilarity. Eight single-nucleotide polymorphisms (SNPs) that were found to have the strongest main effect are reported with the corresponding genes. Four of them conform to previous reports, located in the CDKAL1 gene, while the other 4 SNPs are new findings. Two-order interacting SNP pairs of are also presented. One pair (rs2328549 and rs6486740) has a prominent association, where the two single-nucleotide polymorphism locations are CDKAL1 and GLT1D1. The latter has not been found to have a strong main effect. New findings may result from the proper construction and analysis of a composite trait.