FADS2 Genetic Variance in Combination with Fatty Acid Intake Might Alter Composition of the Fatty Acids in Brain

Multiple lines of evidence suggest that fatty acids (FA) play an important role in cognitive function. However, little is known about the functional genetic pathways involved in cognition. The main goals of this study were to replicate previously reported interaction effects between breast feeding (BF) and FA desaturase (FADS) genetic variation on IQ and to investigate the possible mechanisms by which these variants might moderate BF effect, focusing on brain expression. Using a sample of 534 twins, we observed a trend in the moderation of BF effects on IQ by FADS2 variation. In addition, we made use of publicly available gene expression databases from both humans (193) and mice (93) and showed that FADS2 variants also correlate with FADS1 brain expression (P-value<1.1E-03). Our results provide novel clues for the understanding of the genetic mechanisms regulating FA brain expression and improve the current knowledge of the FADS moderation effect on cognition.     

Integrating environmental covariates and crop modeling into the genomic selection framework to predict genotype by environment interactions

Key message

Development of models to predict genotype by environment interactions, in unobserved environments, using environmental covariates, a crop model and genomic selection. Application to a large winter wheat dataset.

Abstract

Genotype by environment interaction (G*E) is one of the key issues when analyzing phenotypes. The use of environment data to model G*E has long been a subject of interest but is limited by the same problems as those addressed by genomic selection methods: a large number of correlated predictors each explaining a small amount of the total variance. In addition, non-linear responses of genotypes to stresses are expected to further complicate the analysis. Using a crop model to derive stress covariates from daily weather data for predicted crop development stages, we propose an extension of the factorial regression model to genomic selection. This model is further extended to the marker level, enabling the modeling of quantitative trait loci (QTL) by environment interaction (Q*E), on a genome-wide scale. A newly developed ensemble method, soft rule fit, was used to improve this model and capture non-linear responses of QTL to stresses. The method is tested using a large winter wheat dataset, representative of the type of data available in a large-scale commercial breeding program. Accuracy in predicting genotype performance in unobserved environments for which weather data were available increased by 11.1 % on average and the variability in prediction accuracy decreased by 10.8 %. By leveraging agronomic knowledge and the large historical datasets generated by breeding programs, this new model provides insight into the genetic architecture of genotype by environment interactions and could predict genotype performance based on past and future weather scenarios.     

COSTLY SIGNALS IN A FIELD CRICKET CAN INDICATE HIGH‐ OR LOW‐QUALITY DIRECT BENEFITS DEPENDING UPON THE ENVIRONMENT

The handicap hypothesis proposes that male signals provide reliable information to females because only males of high condition provide high‐quality mating benefits and can afford the costs of producing attractive signals. In the context of direct benefits, the handicap hypothesis predicts that benefit quality and signal attractiveness will positively covary among genotypes, positively covary among environments, or be affected by congruent genotype–environment interactions. The latter should occur if the relative condition of a genotype is environment‐dependent. We tested these predictions in the variable field cricket, Gryllus lineaticeps. An interaction between male family and nutritional environment affected the expression of a costly signal preferred by females, while only male family affected direct benefit quality. These noncongruent effects of family and nutritional environment are inconsistent with the handicap hypothesis, and appear to have resulted from variation among nutritional environments in the relationship between signal attractiveness and benefit quality. Surprisingly, signal attractiveness was positively correlated with benefit quality when males experienced a low nutrition environment but negatively correlated with benefit quality when males experienced a high nutrition environment. As a result, female choice for direct benefits may be difficult, particularly in heterogeneous environments, unless females can assess the environmental histories of males.     

FADS2 Polymorphisms Modify the Effect of Breastfeeding on Child IQ

Background

Breastfeeding is important for child cognitive development. A study by Caspi et al has suggested that rs174575 within the FADS2 gene moderates this effect so that children homozygous in the minor allele (GG genotype) have similar IQs irrespective of feeding method.

Methods and Principal Findings

In our study of 5934 children aged 8 years, no genetic main effect with IQ was found for rs174575. However, an interaction with this polymorphism was observed such that breastfed GG children performed better than their formula fed counterparts by an additional 5.8 points [1.4, 10.1] (interaction p = 0.0091). Interaction results were attenuated by about 10% after adjustment for 7 factors. This study also investigated rs1535, another FADS2 polymorphism in linkage disequilibrium with rs174575, together with performance and verbal IQ, finding similar results although effect sizes were generally reduced.

Conclusions and Significance

This study did not replicate the findings of Caspi et al. In contrast to their study, GG children exhibited the greatest difference between feeding methods such that breastfed children performed similarly irrespective of child genotype whereas formula fed GG children performed worse than other children on formula milk. Further studies are required to replicate these findings.     

DNA Methylation, Behavior and Early Life Adversity

The impact of early physical and social environments on life-long phenotypes is well known. Moreover, we have documented evidence for gene–environment interactions where identical gene variants are associated with different phenotypes that are dependent on early life adversity. What are the mechanisms that embed these early life experiences in the genome? DNA methylation is an enzymatically-catalyzed modification of DNA that serves as a mechanism by which similar sequences acquire cell type identity during cellular differentiation and embryogenesis in the same individual. The hypothesis that will be discussed here proposes that the same mechanism confers environmental-exposure specific identity upon DNA providing a mechanism for embedding environmental experiences in the genome, thus affecting long-term phenotypes. Particularly important is the environment early in life including both the prenatal and postnatal social environments.     

Serum vitamins A and E as modifiers of lipid trait genetics in the National Health and Nutrition Examination Surveys as part of the Population Architecture using Genomics and Epidemiology (PAGE) study

Both environmental and genetic factors impact lipid traits. Environmental modifiers of known genotype–phenotype associations may account for some of the “missing heritability” of these traits. To identify such modifiers, we genotyped 23 lipid-associated variants identified previously through genome-wide association studies (GWAS) in 2,435 non-Hispanic white, 1,407 non-Hispanic black, and 1,734 Mexican-American samples collected for the National Health and Nutrition Examination Surveys (NHANES). Along with lipid levels, NHANES collected environmental variables, including fat-soluble macronutrient serum levels of vitamin A and E levels. As part of the Population Architecture using Genomics and Epidemiology (PAGE) study, we modeled gene–environment interactions between vitamin A or vitamin E and 23 variants previously associated with high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglyceride (TG) levels. We identified three SNP?×?vitamin A and six SNP?×?vitamin E interactions at a significance threshold of p?<?2.2?×?10^?3. The most significant interaction was APOB rs693?×?vitamin E (p?=?8.9?×?10^?7) for LDL-C levels among Mexican-Americans. The nine significant interaction models individually explained 0.35–1.61?% of the variation in any one of the lipid traits. Our results suggest that vitamins A and E may modify known genotype–phenotype associations; however, these interactions account for only a fraction of the overall variability observed for HDL-C, LDL-C, and TG levels in the general population.     

Genotype x environment interaction of crossover type: detecting its presence and estimating the crossover point

Genotype-environment interaction (GEI) introduces inconsistency in the relative rating of genotypes across environments and plays a key role in formulating strategies for crop improvement. GEI can be either qualitative (i.e., crossover type) or only quantitative (i.e., non-crossover type). Since the presence of crossover-type interaction has a strong implication for breeding for specific adaptation, it is important to assess the frequency of crossover interactions. This paper presents a test for detecting the presence of crossover-type interaction using the response-environment relationship and enumerates the frequency of crossovers and estimation of the crossover point (CP) on the environment axis, which serves as a cut-off point for the two environments groups where different/specific selections can be made. Sixty-four barley lines with various selection histories were grown in northern Syria and Lebanon giving a total of 21 environments (location-year combinations). Linear regression of the genotypic response on the environmental index represented a satisfactory model, and heterogeneity among regressions was significant. At a 5% level of significance, 38% and 19% of the pairs showed crossover interactions when the error variances were considered heterogeneous and homogeneous, respectively, implying that an appreciable number of crossovers took place in the case of barley lines responding to their environments. The CP of 1.64 t/ha, obtained as the CP of regression lines between the genotype numbers 19 and 31, provided maximum genotype x environment-group interaction. Across all environments, genotype nos. 59 and 12 stood first and second for high yield, respectively. The changes in the ranks of genotypes under the groups of environments can be used for selecting specifically adapted genotypes. Received: 25 January 1999 / Accepted: 16 March 1999     

An epidemiologic approach to ecogenetics.

Although "ecogenetics" seeks to examine genetically mediated differences in susceptibility to environmental agents, researchers often examine the relation between genetic markers and disease without regard to environmental determinants. By using epidemiologic definitions of genotype-environment interaction, it can be shown that the relative risk of disease for the genetic marker is a function of the frequency of exposure to the environmental agent, the strength of interaction between the genotype and the agent, and the specificity of the environmental effect vis-à-vis the genotype. Using examples from the literature, we illustrate under six patterns of genotype-environment interaction that the relative risk associated with the marker can fluctuate markedly. However, with infrequent exposures, the relative risk is close to unity (implying no genetic effect) even in the face of strong genotype-environment interaction. Alternatively, elevated relative risks imply a frequent environmental exposure or a strong pattern of interaction. We suggest that genetic marker-disease associations be evaluated within the context of an epidemiologic study design that considers specific environmental determinants of risk.     

A case-control study between the gene polymorphisms of polyunsaturated fatty acids metabolic rate-limiting enzymes and coronary artery disease in a Chinese Han population

To investigate the association between the polymorphisms of fatty acid desaturase 1 (FADS1), fatty acid desaturase 2 (FADS2) and elongation of very long chain fatty acids like 2 (ELOVL2) gene and coronary artery disease (CAD) in a Chinese Han population. Three single nucleotide polymorphisms (SNPs) from these genes were genotyped using PCR-based restriction fragment length polymorphism analysis in 199 CAD cases and 192 controls of Han Chinese origin. rs174556 in the FADS1 gene showed allelic (P=0.002) and genotypic (P=0.030) association with the disease, while there was no disease association for the other two SNPs. The frequency of rs174556 minor allele (T) was significantly higher in the case group than the control group. The trans phase gene–gene interaction analysis showed that the combined genotype of rs174556 (T/T) and rs3756963 (T/T) was weakly associated with the disease (P=0.043). rs174556 in the FADS1 gene is very likely to be associated with CAD in the Chinese Han population.     

Serotonin transporter gene,childhood emotional abuse and cognitive vulnerability to depression

Meta‐analyses evaluating the association between the serotonin transporter polymorphism (5‐HTTLPR) with neuroticism and depression diagnosis as phenotypes have been inconclusive. We examined a gene–environment interaction on a cognitive vulnerability marker of depression, cognitive reactivity (CR) to sad mood. A total of 250 university students of European ancestry were genotyped for the 5‐HTTLPR, including SNP rs25531, a polymorphism of the long allele. Association analysis was performed for neuroticism, CR and depression diagnosis (using a self‐report measure). As an environmental pathogen, self‐reported history of childhood emotional abuse was measured because of its strong relationship with depression. Participants with the homozygous low expressing genotype had high CR if they had experienced childhood emotional maltreatment but low CR if they did not have such experience. This interaction was strongest on the Rumination subscale of the CR measure. The interaction was not significant with neuroticism or depression diagnosis as outcome measures. Our results show that 5‐HTTLPR is related to cognitive vulnerability to depression. Our findings provide evidence for a differential susceptibility genotype rather than a vulnerability genotype, possibly because of the relatively low levels of abuse in our sample. The selection of phenotype and environmental contributor is pivotal in investigating gene–environment interactions in psychiatric disorders.     

Integrating Crop Growth Models with Whole Genome Prediction through Approximate Bayesian Computation

Genomic selection, enabled by whole genome prediction (WGP) methods, is revolutionizing plant breeding. Existing WGP methods have been shown to deliver accurate predictions in the most common settings, such as prediction of across environment performance for traits with additive gene effects. However, prediction of traits with non-additive gene effects and prediction of genotype by environment interaction (G×E), continues to be challenging. Previous attempts to increase prediction accuracy for these particularly difficult tasks employed prediction methods that are purely statistical in nature. Augmenting the statistical methods with biological knowledge has been largely overlooked thus far. Crop growth models (CGMs) attempt to represent the impact of functional relationships between plant physiology and the environment in the formation of yield and similar output traits of interest. Thus, they can explain the impact of G×E and certain types of non-additive gene effects on the expressed phenotype. Approximate Bayesian computation (ABC), a novel and powerful computational procedure, allows the incorporation of CGMs directly into the estimation of whole genome marker effects in WGP. Here we provide a proof of concept study for this novel approach and demonstrate its use with synthetic data sets. We show that this novel approach can be considerably more accurate than the benchmark WGP method GBLUP in predicting performance in environments represented in the estimation set as well as in previously unobserved environments for traits determined by non-additive gene effects. We conclude that this proof of concept demonstrates that using ABC for incorporating biological knowledge in the form of CGMs into WGP is a very promising and novel approach to improving prediction accuracy for some of the most challenging scenarios in plant breeding and applied genetics.     

Genetic variance of sexually selected traits in waxmoths: maintenance by genotype x environment interaction

When traits experience directional selection, such as that imposed by sexual selection, their genetic variance is expected to diminish. Nonetheless, theory and findings from sexual selection predict and demonstrate that male traits favored by female choice retain substantial amounts of additive genetic variance. We explored this dilemma through an ecological genetic approach and focused on the potential contributions of genotype x environment interaction (GEI) to maintenance of additive genetic variance for male signal characters in the lesser waxmoth, Achroia grisella (Lepidoptera: Pyralidae). We artificially selected genetic variants for two male signal characters, signal rate (SR) and peak amplitude (PA), that influence female attraction and then examined the phenotypic plasticity of these variants (high- and low-SR and high- and low-PA lines) under a range of environmental conditions expected in natural populations. Our split-family breeding experiments indicated that two signal characters, SR and PA, and several developmental characters in both high- and low-SR and high- and low-PA lines displayed considerable phenotypic plasticity among the environments tested. Moreover, strong GEIs leading to crossover between high- and low-SR lines were found for SR and developmental period. Therefore, neither high- nor low-SR genetic variants would achieve maximum attractiveness and fitness in every environment, and those variants producing unattractive signals with low SRs under normal conditions may remain in populations provided that gene flow across environments or generation overlap are sufficiently high. We speculate that the phenotypic plasticity for SR and developmental period is adaptive in A. grisella populations experiencing a range of temperature and density conditions. Females mating with attractive (high-SR) males may be assured of obtaining good genes because these males sire offspring that develop more rapidly and a crossover for developmental period may parallel that for SR. Such parallel crossovers may be expected wherever good-genes sexual selection mechanisms operate.     

Environmental Maternal Effects Mediate the Resistance of Maritime Pine to Biotic Stress

The resistance to abiotic stress is increasingly recognised as being impacted by maternal effects, given that environmental conditions experienced by parent (mother) trees affect stress tolerance in offspring. We hypothesised that abiotic environmental maternal effects may also mediate the resistance of trees to biotic stress. The influence of maternal environment and maternal genotype and the interaction of these two factors on early resistance of Pinus pinaster half-sibs to the Fusarium circinatum pathogen was studied using 10 mother genotypes clonally replicated in two contrasting environments. Necrosis length of infected seedlings was 16% shorter in seedlings grown from favourable maternal environment seeds than in seedlings grown from unfavourable maternal environment seeds. Damage caused by F. circinatum was mediated by maternal environment and maternal genotype, but not by seed mass. Mechanisms unrelated to seed provisioning, perhaps of epigenetic nature, were probably involved in the transgenerational plasticity of P. pinaster, mediating its resistance to biotic stress. Our findings suggest that the transgenerational resistance of pines due to an abiotic stress may interact with the defensive response of pines to a biotic stress.     

Effects of data structure on the estimation of covariance functions to describe genotype by environment interactions in a reaction norm model

Covariance functions have been proposed to predict breeding values and genetic (co)variances as a function of phenotypic within herd-year averages (environmental parameters) to include genotype by environment interaction. The objective of this paper was to investigate the influence of definition of environmental parameters and non-random use of sires on expected breeding values and estimated genetic variances across environments. Breeding values were simulated as a linear function of simulated herd effects. The definition of environmental parameters hardly influenced the results. In situations with random use of sires, estimated genetic correlations between the trait expressed in different environments were 0.93, 0.93 and 0.97 while simulated at 0.89 and estimated genetic variances deviated up to 30% from the simulated values. Non random use of sires, poor genetic connectedness and small herd size had a large impact on the estimated covariance functions, expected breeding values and calculated environmental parameters. Estimated genetic correlations between a trait expressed in different environments were biased upwards and breeding values were more biased when genetic connectedness became poorer and herd composition more diverse. The best possible solution at this stage is to use environmental parameters combining large numbers of animals per herd, while losing some information on genotype by environment interaction in the data.     

Frameworks of population obesity and the use of cultural consensus modeling in the study of environments contributing to obesity

Obesity in Eastern Europe has been linked to privilege and status prior to the collapse of communism, and to exposure to free-market economics after it. Neither formulation is a complete explanation, and it is useful to examine the potential value of other models of population obesity for the understanding of this phenomenon. These include those of: thrifty genotypes; obesogenic behaviour; obesogenic environments; nutrition transition; obesogenic culture; and biocultural interactions of genetics, environment, behaviour and culture. At the broadest level, obesity emerges from the interaction of thrifty genotype with obesogenic environment. However, defining obesogenic environments remains problematic, especially in relation to sociocultural factors. Furthermore, since different identity groups may share different values concerning the obesogenicity of the environment, a priori assumptions about group homogeneity may lead to flawed interpretations of the importance of sociocultural factors in obesogenic environments. A new way to identify cultural coherence of groups and populations in relation to environments contributing to obesity is put forward here, that of cultural consensus modeling.     

Performance of hybrid poplar clones in short rotation coppice in Mediterranean environments: analysis of genotypic stability

Improving production in short rotation coppice (SRC) plantations requires, among other elements, a proper understanding of clonal performance. Genotypic stability over a range of environments is a factor of concern for breeding and recommendation purposes. Most common stability measures can be embedded in a mixed‐model framework accounting for interaction and heterocedasticity in genotype‐by‐environment tables. Data from nine hybrid poplars of different taxonomic background were tested in four Mediterranean sites under three agronomic practices (control, herbicide application, and supplementary fertilization) for total biomass (TB), stem biomass (SB), and branch biomass (BB) at the end of the first rotation. Stability models (stability variance, Finlay–Wilkinson and Eberhart–Russell) were compared, also allowing for the definition of groups of genotypes with distinct taxonomic backgrounds and a priori different variabilities. Results showed that genotype‐by‐environment (GE) interactions were associated with factors inherent to evaluation sites rather than to the agronomic practices tested. Depending on biomass fraction, regression models provided appropriate stability measures. Highly reactive clones to improving environmental conditions (e.g., ‘AF2’) tended to show the largest mean TB. However, this was not always the case, as clone ‘Monviso’ showed both intermediate reactivity (i.e., stable sensu Eberhart–Russell) and enhanced overall performance. The taxonomic group was relevant for explaining stability patterns for SB. The stability assessment for BB indicated different patterns in biomass allocation. Present findings point to the feasibility of either exploiting specific adaptation (in which case hybrid type may play a relevant role) or searching for broadly adapted, stable material exhibiting good performance in Mediterranean conditions.     

Exploring the etiology of the association between birthweight and IQ in an adolescent twin sample.

The negative effects of very low birthweight on intellectual development have been well documented, and more recently this effect has been shown to generalize to birthweights within the normal range. In this study we investigate the etiology of this relationship by using a classical twin design to disentangle the contributions of genes and environment. A previous Dutch study (Boomsma et al., 2001) examining these effects indicated that genes were important in mediating the association of birthweight to full IQ measured at ages 7 and 10, but not at ages 5 and 12. Here the association between birthweight and IQ at age 16 is considered (N = 523 twin pairs). Using variance components modeling we found that the genetic variance in birthweight (4%) completely overlapped with that in verbal IQ but not performance or full IQ. Results further showed the importance of shared environmental effects on birthweight (~ 60%) but not on IQ (with genes explaining up to 72% of IQ variance). Models incorporating a direction of causation parameter between birthweight and IQ provided adequate fit to the data in either causal direction for performance and full IQ, but the model with verbal IQ causing birthweight was preferred to one in which birthweight influenced verbal IQ. As the measurement of birthweight precedes the measurement of twins' IQ at age 16, the influence of verbal IQ might be better considered as a proxy for parents' IQ or education, and it is possible that brighter mothers provide better prenatal environments for their children.