Evidence of Shared Genome-Wide Additive Genetic Effects on Interpersonal Trauma Exposure and Generalized Vulnerability to Drug Dependence in a Population of Substance Users

AbstractIn statistical genetics an important task involves building predictive models for the genotype-phenotype relationships and thus attribute a proportion of the total phenotypic variance to the variation in genotypes. Numerous models have been proposed to incorporate additive genetic effects into models for prediction or association. However, there is a scarcity of models that can adequately account for gene by gene or other forms of genetical interactions. In addition, there is an increased interest in using marker annotations in genome-wide prediction and association. In this paper, we discuss an hybrid modeling methodology which combines the parametric mixed modeling approach and the non-parametric rule ensembles. This approach gives us a flexible class of models that can be used to capture additive, locally epistatic genetic effects, gene x background interactions and allows us to incorporate one or more annotations into the genomic selection or association models. We use benchmark data sets covering a range of organisms and traits in addition to simulated data sets to illustrate the strengths of this approach. The improvement of model accuracies and association results suggest that a part of the ’’missing heritability” in complex traits can be captured by modeling local epistasis.

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Genome-wide scan reveals important additive and non-additive genetic effects associated with resistance to Haemonchus contortus in Florida Native sheep

International Journal for Parasitology ◽

10.1016/j.ijpara.2020.11.003 ◽

2021 ◽

Author(s):

Zaira M. Estrada-Reyes ◽

D. Owen Rae ◽

Raluca G. Mateescu

Keyword(s):

Haemonchus Contortus ◽

Genetic Effects ◽

Genome Wide ◽

Native Sheep ◽

Additive Genetic Effects ◽

Genome Wide Scan

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Combining Ability of Plant Height and Yield components in Indian Mustard (Brassica junceaL.Czern & Coss.) under Salt affected Soil using Line×Tester Analysis

Journal of AgriSearch ◽

10.21921/jas.v3i2.11267 ◽

2016 ◽

Vol 3 (2) ◽

Cited By ~ 2

Author(s):

SHAILESH CHAND GAUTAM ◽

MP Chauhan

Keyword(s):

Plant Height ◽

Seed Yield ◽

Combining Ability ◽

Yield Components ◽

Indian Mustard ◽

Heritability Estimate ◽

Genetic Effects ◽

Narrow Sense ◽

Narrow Sense Heritability ◽

Additive Genetic Effects

Line × tester analysis of twenty lines and three testers of Indian mustard (Brassica juncea L. Czern & Coss.) cultivars were used to estimate general combining ability (GCA), specific combining ability (SCA) effects, high parent heterosis and narrow-sense heritability estimate for plant height, yield components and seed yield. Significant variance of line x tester for the traits like pods per plant and seed yield indicating non additive genetic effects have important role for controlling these traits. Significant mean squares of parents v/s crosses which are indicating significant average heterosis were also significant for all the traits except seeds per pod. High narrow-sense heritability estimates for all the traits except seeds per pod exhibited the prime importance of additive genetic effects for these traits except seeds per pod. Most of the crosses with negative SCA effect for plant height had at least one parent with significant negative or negative GCA effect for this trait. For most of the traits except pods per plant, the efficiency of high parent heterosis effect was more than SCA effect for determining superior cross combinations.

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Genomic prediction with non-additive effects in beef cattle: stability of variance component and genetic effect estimates against population size

BMC Genomics ◽

10.1186/s12864-021-07792-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Akio Onogi ◽

Toshio Watanabe ◽

Atsushi Ogino ◽

Kazuhito Kurogi ◽

Kenji Togashi

Keyword(s):

Population Size ◽

Genomic Prediction ◽

Variance Components ◽

Variance Component ◽

Predictive Accuracy ◽

Genetic Effect ◽

Genetic Effects ◽

Additive Effects ◽

Additive Variance ◽

Additive Genetic Effects

Abstract Background Genomic prediction is now an essential technology for genetic improvement in animal and plant breeding. Whereas emphasis has been placed on predicting the breeding values, the prediction of non-additive genetic effects has also been of interest. In this study, we assessed the potential of genomic prediction using non-additive effects for phenotypic prediction in Japanese Black, a beef cattle breed. In addition, we examined the stability of variance component and genetic effect estimates against population size by subsampling with different sample sizes. Results Records of six carcass traits, namely, carcass weight, rib eye area, rib thickness, subcutaneous fat thickness, yield rate and beef marbling score, for 9850 animals were used for analyses. As the non-additive genetic effects, dominance, additive-by-additive, additive-by-dominance and dominance-by-dominance effects were considered. The covariance structures of these genetic effects were defined using genome-wide SNPs. Using single-trait animal models with different combinations of genetic effects, it was found that 12.6–19.5 % of phenotypic variance were occupied by the additive-by-additive variance, whereas little dominance variance was observed. In cross-validation, adding the additive-by-additive effects had little influence on predictive accuracy and bias. Subsampling analyses showed that estimation of the additive-by-additive effects was highly variable when phenotypes were not available. On the other hand, the estimates of the additive-by-additive variance components were less affected by reduction of the population size. Conclusions The six carcass traits of Japanese Black cattle showed moderate or relatively high levels of additive-by-additive variance components, although incorporating the additive-by-additive effects did not improve the predictive accuracy. Subsampling analysis suggested that estimation of the additive-by-additive effects was highly reliant on the phenotypic values of the animals to be estimated, as supported by low off-diagonal values of the relationship matrix. On the other hand, estimates of the additive-by-additive variance components were relatively stable against reduction of the population size compared with the estimates of the corresponding genetic effects.

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Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability

Nature Communications ◽

10.1038/s41467-020-19366-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Vasiliki Lagou ◽

◽

Reedik Mägi ◽

Jouke- Jan Hottenga ◽

Harald Grallert ◽

...

Keyword(s):

Genome Wide Association Study ◽

Fasting Glucose ◽

Genetic Correlations ◽

Epidemiological Studies ◽

Genetic Effects ◽

Fasting Insulin ◽

Sex Dimorphism ◽

Waist To Hip Ratio ◽

Genome Wide ◽

Meta Analyses

AbstractDifferences between sexes contribute to variation in the levels of fasting glucose and insulin. Epidemiological studies established a higher prevalence of impaired fasting glucose in men and impaired glucose tolerance in women, however, the genetic component underlying this phenomenon is not established. We assess sex-dimorphic (73,089/50,404 women and 67,506/47,806 men) and sex-combined (151,188/105,056 individuals) fasting glucose/fasting insulin genetic effects via genome-wide association study meta-analyses in individuals of European descent without diabetes. Here we report sex dimorphism in allelic effects on fasting insulin at IRS1 and ZNF12 loci, the latter showing higher RNA expression in whole blood in women compared to men. We also observe sex-homogeneous effects on fasting glucose at seven novel loci. Fasting insulin in women shows stronger genetic correlations than in men with waist-to-hip ratio and anorexia nervosa. Furthermore, waist-to-hip ratio is causally related to insulin resistance in women, but not in men. These results position dissection of metabolic and glycemic health sex dimorphism as a steppingstone for understanding differences in genetic effects between women and men in related phenotypes.

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The expression of additive and nonadditive genetic variation under stress.

Genetics ◽

10.1093/genetics/140.3.1149 ◽

1995 ◽

Vol 140 (3) ◽

pp. 1149-1159

Author(s):

M W Blows ◽

M B Sokolowski

Keyword(s):

Genetic Variation ◽

Development Time ◽

Genetic Effects ◽

Hybrid Breakdown ◽

Bristle Number ◽

Gene Complexes ◽

General Expectation ◽

Faster Development ◽

Seven Generations ◽

Additive Genetic Effects

Abstract Experimental lines of Drosophila melanogaster derived from a natural population, which had been isolated in the laboratory for approximately 70 generations, were crossed to determine if the expression of additive, dominance and epistatic genetic variation in development time and viability was associated with the environment. No association was found between the level of additive genetic effects and environmental value for either trait, but nonadditive genetic effects increased at both extremes of the environmental range for development time. The expression of high levels of dominance and epistatic genetic variation at environmental extremes may be a general expectation for some traits. The disruption of the epistatic gene complexes in the parental lines resulted in hybrid breakdown toward faster development and there was some indication of hybrid breakdown toward higher viability. A combination of genetic drift and natural selection had therefore resulted in different epistatic gene complexes being selected after approximately 70 generations from a common genetic base. After crossing, the hybrid populations were observed for 10 generations. Epistasis contributed on average 12 hr in development time. Fluctuating asymmetry in sternopleural bristle number also evolved in the hybrid populations, decreasing by > 18% in the first seven generations after hybridization.

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Estimates of additive genetic effects, maternal effects, specific combining ability, maternal heterosis, and egg cytoplasm effects for cold tolerance in Oreochromis niloticus (L.)

Aquaculture Research ◽

10.1111/j.1365-2109.1989.tb00340.x ◽

1989 ◽

Vol 20 (2) ◽

pp. 159-166 ◽

Cited By ~ 2

Author(s):

D. TAVE ◽

R.O. SMITHERMAN ◽

V. JAYAPRAKAS

Keyword(s):

Cold Tolerance ◽

Maternal Effects ◽

Oreochromis Niloticus ◽

Combining Ability ◽

Genetic Effects ◽

Specific Combining Ability ◽

Additive Genetic Effects

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Association between Griffing's diallel and the adaptability and stability of Eberhart and Russel

Genetics and Molecular Biology ◽

10.1590/s1415-47571999000300027 ◽

1999 ◽

Vol 22 (3) ◽

pp. 451-456 ◽

Cited By ~ 5

Author(s):

Cleso Antônio Patto Pacheco ◽

Cosme Damião Cruz ◽

Manoel Xavier dos Santos

Keyword(s):

Combining Ability ◽

General Combining Ability ◽

Genetic Effects ◽

Specific Combining Ability ◽

Regression Coefficients ◽

Stability Parameters ◽

The Mean ◽

Additive Genetic Effects ◽

F1 Cross

The objective of the present work was to provide a methodology to study the inheritance of adaptability and stability through the breakdown of Eberhart and Russell regression coefficients and regression deviations in effects due to the mean and additive genetic effects (gi's and gj's) as well as dominance effects (sij's) of Griffing´s methodology, when the diallel is conducted in several environments. It was concluded that the adaptability and stability parameters are determined in the same manner as are genetic effects. So an F1 cross inherits half the general combining ability (GCA) mean effect from each parent, while the effects due to specific combining ability (SCA) are subjected to the same considerations relative to sij's, i.e., they are dependent on specific combinations.

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