• Genomics & Informatics
• /
• 제20권1호
• /
• pp.9.1-9.6
• /
• 2022

Mendelian randomization (MR) uses genetic variation as a natural experiment to investigate the causal effects of modifiable risk factors (exposures) on outcomes. Two-sample Mendelian randomization (2SMR) is widely used to measure causal effects between exposures and outcomes via genome-wide association studies. 2SMR can increase statistical power by utilizing summary statistics from large consortia such as the UK Biobank. However, the first-order term approximation of standard error is commonly used when applying 2SMR. This approximation can underestimate the variance of causal effects in MR, which can lead to an increased false-positive rate. An alternative is to use the second-order approximation of the standard error, which can considerably correct for the deviation of the first-order approximation. In this study, we simulated MR to show the degree to which the first-order approximation underestimates the variance. We show that depending on the specific situation, the first-order approximation can underestimate the variance almost by half when compared to the true variance, whereas the second-order approximation is robust and accurate.

• Journal of Ecology and Environment
• /
• 제45권3호
• /
• pp.97-104
• /
• 2021

Background: Asarum sieboldii Miq., a species of forest understory vegetation, is an herbaceous perennial belonging to the family Aristolochiaceae. The metapopulation of A. sieboldii is distributed sparsely and has a short seed dispersal distance by ants as their seed distributor. It is known that many flowers of A. sieboldii depend on self-fertilization. Because these characteristics can affect negatively in genetic structure, investigating habitat structure and assessment of genetic structure is needed. A total of 27 individuals in a valley were sampled for measuring genetic diversity, genetic distance, and genetic differentiation by RAPDPCR. Results: The habitat areas of A. sieboldii metapopulation were relatively small (3.78~33.60 m²) and population density was very low (five to seven individuals in 20×20 m quadrat). The habitat of A. sieboldii was a very shady (relative light intensity = 0.9%) and mature forest with a high evenness value (J = 0.81~0.99) and a low dominance value (D = 0.19~0.28). The total genetic diversity of A. sieboldii was quite high (h = 0.338, I = 0.506). A total of 33 band loci were observed in five selected primers, and 31 band loci (94%) were polymorphic. However, genetic differentiation along the valley was highly progressed (G_st = 0.548, N_m = 0.412). The average genetic distance between subpopulations was 0.387. The results of AMOVA showed 52.77% of variance occurs among populations, which is evidence of population structuring. Conclusions: It is expected that a small-scale founder effect had occurred, an individual spread far from the original subpopulation formed a new subpopulation. However, geographical distance between individuals would have been far and genetic flow occurred only within each subpopulation because of the low density of population. This made significant genetic distance between the original and new population by distance. Although genetic diversity of A. sieboldii metapopulation is not as low as concerned, the subpopulation of A. sieboldii can disappear by stochastic events due to small subpopulation size and low density of population. To prevent genetic isolation and to enhance the stable population size, conservative efforts such as increasing the size of each subpopulation or the connection between subpopulations are needed.

• Journal of Animal Science and Technology
• /
• 제48권6호
• /
• pp.759-766
• /
• 2006

본 연구는 농협중앙회 가축개량사업소가 보유하고 있는 1998년부터 2005년까지 실시한 한우 당대검정 대상우 2,532두의 자료와 1996년부터 2002년까지 실시한 한우 후대검정 대상우 1,819두의 자료를 이용하여 당대 및 후대의 형질을 다형질 개체모형을 이용하여 유전모수를 추정하였다. 적합한 통계분석모형을 찾기 위하여 각 형질별로 회귀분석을 통한 변수선택방법으로 고정효과와 공변량을 결정하고, MTDFREML 패키지를 이용하여 유전모수를 추정하였다. 분석형질은 등지방두께, 도체중, 도체율, 등심단면적, 근내지방도 및 12개월령 체중으로, 이들의 유전력은 각각 0.51, 0.32, 0.27, 0.33, 0.50 및 0.26로 나타났다. 한편 유전평가에서 제외되었던 등지방두께 및 도체율의 유전력이 각각 0.51 및 0.27으로 추정되어 이에 대한 선발이 가능할 것으로 나타났다. 특히 등지방두께는 현 육량지수 산출식에서 그 영향력이 매우 크므로 한우보증씨수소 선발지수에 포함하는 방안을 고려할 필요가 있을 것으로 사료된다. 도체형질간의 유전상관은 등지방두께와 등심단면적을 제외하고 모두 양의 상관을 나타났다. 그러나, 12개월령 보정체중과 도체율 및 근내지방도의 유전상관은 각각 0.09 및 0.27으로 나타나 현행 한우개량체계에서 처럼 당대검정우를 12개월령 체중으로 선발할 경우 등심단면적과 근내지방도가 우수한 개체가 탈락할 가능성이 있는 것으로 나타나 이의 보완을 위한 혈통지수의 활용방안이나 초음파단층촬영기술의 이용방법에 대한 추가연구가 필요한 것으로 사료된다.

• 한국자원식물학회지
• /
• 제27권6호
• /
• pp.660-670
• /
• 2014

The Korean plum yew (Cephalotaxus koreana Nakai) is a shade-tolerant, coniferous shrub. The seeds have been used as a folk medicine in Korea, and an alkaloid extract (HTT) is known to have anticancer properties. We estimated the genetic diversity of 429 trees in 16 populations in South Korea using 194 polymorphic amplicons from seven combinations of AFLP primer-restriction enzymes. The average number of effective alleles and the percentage of polymorphic loci were 1.37 and 79.4%, respectively. Shannon's diversity index and the expected heterozygosity were 0.344 and 0.244, respectively. We divided 16 populations into four groups on the UPGMA dendrogram and the PCA biplot. The first two principal components explained 84% of the total genetic variation. Genetic differentiation between populations explained 14% of total genetic variation, and the remaining 86% came from difference between individuals within populations, as determined by an analysis of molecular variance (AMOVA). However, the genetic differentiation did not correlate with the geographic distance between populations from the Mantel test. The Bayesian statistics, which are comparable to Wright's $F_{ST}$ and Nei's $G_{ST}$, were ${\theta}^I=0.406$ and ${\theta}^{II}=0.172$, respectively. The population genetic diversity was slightly lower, and the strength of genetic differentiation was much weaker, than the average of those plants having similar life histories, as assessed using arbitrary marker systems. We discuss strategies for the genetic conservation of the plum yew in Korea.

• 한국가금학회지
• /
• 제25권1호
• /
• pp.1-9
• /
• 1998

This study was carried out to get the basic and applicable data for breeding plan and selection in order to improve the body shape components in Korean native chicken. The hentabilities and genetic correlations on body shape components were estimated by sire, dam and combined components of variance. Data analyzed were records of 1,096 progenies produced from 180 dams and 26 sires from April, 1994 to September, 1995. On body shape components at 4, 8 and 16 weeks of age, the shank lengths were 55.63, 82.94 and 103.8Omm: breast girths were 15.087, 21.069, and 26.137mm: breast widths were 40.910, 54.575 and 73.088mm, respectively. The estimates of hentabilities of body shape components based on the variance of sires, dams, and combined components at 4, 8 and 16 weeks of age were O.O65~O.197, O.25O~O.794 and O.185~O.495 for shank length: O.123~O. 215, O.033~O.513 and 0.063~0.257 for breast girth; 0.024~0.158, 0.118~0.410 and 0.111~0.222 for breast width, respectively. The coefficients of genetic correlations among the body shape components at 4 weeks of age were 0.565, 0.725 and 0.678 for breast girth with breast width, shank length and tibia length : 0.690 and 0.804 for breast width with shank length and tibia length; 0.972 between shank length and tibia length.

• 한국작물학회지
• /
• 제31권2호
• /
• pp.179-185
• /
• 1986

구기자 육종의 수량형질에 대한 선발효율을 높이기 위한 기초연구로서 유전력, 표현형 상관, 유전상관, 환경상관 및 경노계수에 대해 연차간 유전통계량을 분석한 결과를 요약하면 다음과 같다. 1. 포기자의 수양형질중 생과중, 건과중 및 생근중의 유전분산이 가장 크고 년차간의 변동이 적었으며 기타의 형질도 유전분산이 환경분산보다는 컸고 연차간변동은 적었다. 2. 3개년간 전품종들을 Pool로 한 분석에서 연차와 품종 및 이들의 교호작용은 건과율 및 건근중률을 제외한 모든 수양형질에서 고도의 유의차가 인정되었으며 연차간변동도 적었다. 3. 광의의 유전력에서는 생과중, 건과중, 생근중, 건근중 및 지골피수량양에서 매우 높았고 연차간변동도 적었다. 4. 유전상관에서는 생과중과 건과중, 생근중과 지골피, 생근중과 지골피비율, 건근중과 지골피간에는 고도의 정의 상관으로 유의성도 높고 연차간의 변동도 적 었다. 5. 경노계수의 연차간변동은 대체로 적었으나 3개년간 모두 지골피수량에 직접, 간접으로 효과를 크게 미치는 형질은 생근중이었다.

• Asian-Australasian Journal of Animal Sciences
• /
• 제21권5호
• /
• pp.633-639
• /
• 2008

The genetic relationship of gestation length (GL) with birth and weaning weight (BW, WW) was investigated using data collected from the Hanwoo Experiment Station, National Institute of Animal Science, RDA, Republic of Korea. Analytical mixed models including birth year‐season, sex of calf, linear and quadratic covariates of age of dam (days) and linear covariate of age at weaning (days) as fixed effects were used. Corresponding restricted maximum likelihood (REML) and Bayesian estimates of variance components and heritability were obtained with two models; Model 1 included only direct genetic effect and Model 2 included direct genetic, maternal genetic and permanent environmental effect. All the genetic parameter estimates from REML were corresponding to the Bayesian estimates. Direct heritability estimates for GL, BW, and WW were 0.48, 0.33 and 0.25 by Model 1. From Model 2, direct and maternal heritability estimates were 0.38 and 0.03 for GL, 0.14 and 0.05 for BW, and 0.08 and 0.05 for WW. Genetic correlation estimates between direct and maternal effects were 0.05 for GL, 0.59 for BW, and 0.52 for WW. Estimates of direct genetic correlation between GL and BW (WW) were 0.44 (0.21). Positive genetic correlation of GL with BW and WW imply that selection for greater BW or WW would lead to prolonged gestation length.

• Asian-Australasian Journal of Animal Sciences
• /
• 제12권5호
• /
• pp.677-681
• /
• 1999

Estimates were made of genetic parameters for average daily gain (ADG) and average backfat thickness (ABF), and of the effect of sex on estimates of variance-covariance components for average daily gain of boars (DGM) and gilts (DGF) and average bacfat thickness of boars (BFM) and gilts (BFF) by residual maximum likelihood (REML) under a bivariate animal model. Data included a total of 2233 records (757 for boars and 1476 for gilts) of the Large White breed born between 1981 and 1986 in Miyazaki and Iwate prefectures in Japan. Heritability estimates for ADG and ABF were 0.43 and 0.69, respectively, with a genetic correlation of -0.08. Heritability estimates for DGM and DGF were 0.54 and 0.46, respectively, with a genetic correlation of 0.79, including that the two traits are influenced by similar but not identical genes. Respective estimates for BFM and BFF were 0.71 and 0.72 with a genetic correlation of 0.95, indicating that identical genes influence backfat thickness in boars and gilts.

• 한국수산과학회지
• /
• 제42권6호
• /
• pp.600-603
• /
• 2009

Genetic and phenotypic parameter estimates for measurement traits were obtained from pacific oyster Crassostrea gigas at nine months old. For the growth-related traits among nine months old pacific oyster, heritabilities of shell length, shell height, shell width, total weight, body weight and shell weight were estimated as 0.4855, 0.5248, 0.0884, 0.7236, 0.7726 and 0.6957, respectively. Genetic correlations among the growth-related traits of pacific oyster at nines month old, shell length, shell height, shell width, total weight, body weight, shell weight were showing highly positive correlations. Breeding value on growth-related traits of pacific oyster at nine months old were estimated as shell length -7.044-11.870, shell height -11.380-18.370, shell width -1.234-2.831, total weight -8.339-17.140, body weight -1.813-3.507 and shell weight -4.422-8.837. The results show that there is quite substantial additive genetic variance for measurement traits in pacific oyster that can be exploited through selective breeding.

• 한국환경농학회지
• /
• 제33권1호
• /
• pp.37-43
• /
• 2014

BACKGROUND: Water quality data are collected less frequently than flow data because of the cost to collect and analyze, while water quality data corresponding to flow data are required to compute pollutant loads or to calibrate other hydrology models. Regression models are applicable to interpolate water quality data corresponding to flow data. METHODS AND RESULTS: A regression model was suggested which is capable to consider flow and time variance, and the regression model coefficients were calibrated using various measured water quality data with genetic-algorithm. Both LOADEST and the regression using genetic-algorithm were evaluated by 19 water quality data sets through calibration and validation. The regression model using genetic-algorithm displayed the similar model behaviors to LOADEST. The load estimates by both LOADEST and the regression model using genetic-algorithm indicated that use of a large proportion of water quality data does not necessarily lead to the load estimates with smaller error to measured load. CONCLUSION: Regression models need to be calibrated and validated before they are used to interpolate pollutant loads, as separating water quality data into two data sets for calibration and validation.