Candidate gene-environment interaction research: reflections and recommendations

Studying how genetic predispositions come together with environmental factors to contribute to complex behavioral outcomes has great potential for advancing the understanding of the development of psychopathology. It represents a clear theoretical advance over studying these factors in isolation. However, research at the intersection of multiple fields creates many challenges. We review several reasons why the rapidly expanding candidate gene-environment interaction (cG×E) literature should be considered with a degree of caution. We discuss lessons learned about candidate gene main effects from the evolving genetics literature and how these inform the study of cG×E. We review the importance of the measurement of the gene and environment of interest in cG×E studies. We discuss statistical concerns with modeling cG×E that are frequently overlooked. Furthermore, we review other challenges that have likely contributed to the cG×E literature being difficult to interpret, including low power and publication bias. Many of these issues are similar to other concerns about research integrity (e.g., high false-positive rates) that have received increasing attention in the social sciences. We provide recommendations for rigorous research practices for cG×E studies that we believe will advance its potential to contribute more robustly to the understanding of complex behavioral phenotypes.

Gene environment interaction studies in depression and suicidal behavior: An update

Increasing evidence supports the involvement of both heritable and environmental risk factors in major depression (MD) and suicidal behavior (SB). Studies investigating gene-environment interaction (G × E) may be useful for elucidating the role of biological mechanisms in the risk for mental disorders. In the present paper, we review the literature regarding the interaction between genes modulating brain functions and stressful life events in the etiology of MD and SB and discuss their potential added benefit compared to genetic studies only. Within the context of G × E investigation, thus far, only a few reliable results have been obtained, although some genes have consistently shown interactive effects with environmental risk in MD and, to a lesser extent, in SB. Further investigation is required to disentangle the direct and mediated effects that are common or specific to MD and SB. Since traditional G × E studies overall suffer from important methodological limitations, further effort is required to develop novel methodological strategies with an interdisciplinary approach.

Should we treat the ionome as a combination of individual elements, or should we be deriving novel combined traits?

It has been more than 10 years since the concept of the ionome, all of the mineral nutrients in a cell tissue or organism, was introduced. In the intervening years, ionomics, high throughput elemental profiling, has been used to analyse over 400,000 samples from at least 10 different organisms. There are now multiple published examples where an ionomics approach has been used to find genes of novel function, find lines or environments that produce foods with altered nutritional profiles, or define gene by environmental effects on elemental accumulation. In almost all of these studies, the ionome has been treated as a collection of independent elements, with the analysis repeated on each measured element. However, many elements share chemical properties, are known to interact with each other, or have been shown to have similar interactions with biological molecules. Accordingly, there is strong evidence from ionomic studies that the elements of the ionome do not behave independently and that combinations of elements should be treated as the phenotypes of interest. In this review, I will consider the evidence that we have for the interdependence of the ionome, some of its causes, methods for incorporating this interdependence into analyses and the benefits, drawbacks, and challenges of taking these approaches.

Genetics of complex traits in psychiatry

Virtually all psychiatric traits are genetically complex. This article discusses the genetics of complex traits in psychiatry. The complexity is accounted for by numerous factors, including multiple risk alleles, epistasis, and epigenetic effects such as methylation. Risk alleles can individually be common or rare, and can include, for example, single nucleotide polymorphisms and copy number variants that are transmitted or are new mutations, and other kinds of variation. Many different kinds of variation can be important for trait risk, either together in various proportions or as different factors in different subjects. Until more recently, approaches to complex traits were limited, and consequently only a few variants, usually of individually minor effect, were identified. At the present time, a much richer armamentarium exists that includes the routine application of genome-wide association studies and next-generation high-throughput sequencing and the combination of this information with other biologically relevant information, such as expression data. We have also seen the emergence of large meta-analysis and mega-analysis consortia. These developments are extremely important for psychiatric genetics, have advanced the field substantially, and promise formidable gains in the years to come as they are applied more widely.

Interaction between lifestyle and genetic susceptibility in myopia: the Generation R study

Myopia is a refractive error of the eye caused by a complex interplay between nature and nurture. The aim of this study was to investigate whether environmental risk factors can influence the genetic effect in children developing myopia. A total of 3422 children participating in the birth-cohort study Generation R underwent an extensive eye examination at 9 years with measurements of refractive error and axial length corneal radius ratio (AL/CR). Environmental risk factors were evaluated using a questionnaire, and environmental risk scores (ERS) were calculated using backward regression analyses. Genetic risk scores (GRS) were calculated based on all currently known risk variants for myopia. Gene-environment interaction (G×E) was investigated using linear and logistic regression analyses. The predictive value of G×E and parental myopia was estimated using receiver operating characteristic curves. Myopia prevalence was 12%. Both GRS (P < 0.01) and ERS (P < 0.01) were significantly associated with myopia and AL/CR, as was G×E interaction (P < 0.01 for myopia; P = 0.07 for AL/CR). The predictive value of parental myopia was 0.67 (95% CI 0.65–0.70), similar to the values of GRS (0.67; 95% CI 0.64–0.70; P = 0.98) and ERS (0.69; 95% CI 0.66–0.72; P = 0.98). Adding G×E interaction significantly improved the predictive value to 0.73 (95% CI 0.70–0.75; P < 0.01). This study provides evidence that nature and nurture are equally important for myopia and AL/CR; however, the combination has the strongest influence. Since myopia genes are common in the population, adjustment of lifestyle should be a major focus in the prevention of myopia.

Genetic influences on conduct disorder

Conduct disorder (CD) is a moderately heritable psychiatric disorder of childhood and adolescence characterized by aggression toward people and animals, destruction of property, deceitfulness or theft, and serious violation of rules. Genome-wide scans using linkage and association methods have identified a number of suggestive genomic regions that are pending replication. A small number of candidate genes (e.g., GABRA2, MAOA, SLC6A4, AVPR1A) are associated with CD related phenotypes across independent studies; however, failures to replicate also exist. Studies of gene-environment interplay show that CD genetic predispositions also contribute to selection into higher-risk environments, and that environmental factors can alter the importance of CD genetic factors and differentially methylate CD candidate genes. The field's understanding of CD etiology will benefit from larger, adequately powered studies in gene identification efforts; the incorporation of polygenic approaches in gene-environment interplay studies; attention to the mechanisms of risk from genes to brain to behavior; and the use of genetically informative data to test quasi-causal hypotheses about purported risk factors.

Quantitative trait loci and candidate genes underlying genotype by environment interaction in the response of Arabidopsis thaliana to drought

Drought stress was imposed on two sets of Arabidopsis thaliana genotypes grown in sand under short-day conditions and analysed for several shoot and root growth traits. The response to drought was assessed for quantitative trait locus (QTL) mapping in a genetically diverse set of Arabidopsis accessions using genome-wide association (GWA) mapping, and conventional linkage analysis of a recombinant inbred line (RIL) population. Results showed significant genotype by environment interaction (G×E) for all traits in response to different watering regimes. For the RIL population, the observed G×E was reflected in 17 QTL by environment interactions (Q×E), while 17 additional QTLs were mapped not showing Q×E. GWA mapping identified 58 single nucleotide polymorphism (SNPs) associated with loci displaying Q×E and an additional 16 SNPs associated with loci not showing Q×E. Many candidate genes potentially underlying these loci were suggested. The genes for RPS3C and YLS7 were found to contain conserved amino acid differences when comparing Arabidopsis accessions with strongly contrasting drought response phenotypes, further supporting their candidacy. One of these candidate genes co-located with a QTL mapped in the RIL population.

Rice breeding for yield under drought has selected for longer flag leaves and lower stomatal density

Direct selection for yield under drought has resulted in the release of a number of drought-tolerant rice varieties across Asia. In this study, we characterized the physiological traits that have been affected by this strategy in breeding trials across sites in Bangladesh, India, and Nepal. Drought- breeding lines and drought-tolerant varieties showed consistently longer flag leaves and lower stomatal density than our drought-susceptible check variety, IR64. The influence of environmental parameters other than drought treatments on leaf traits was evidenced by close grouping of treatments within a site. Flag-leaf length and width appeared to be regulated by different environmental parameters. In separate trials in the Philippines, the same breeding lines studied in South Asia showed that canopy temperature under drought and harvest index across treatments were most correlated with grain yield. Both atmospheric and soil stress strengthened the relationships between leaf traits and yield. The stable expression of leaf traits among genotypes and the identification of the environmental conditions in which they contribute to yield, as well as the observation that some breeding lines showed longer time to flowering and higher canopy temperature than IR64, suggest that selection for additional physiological traits may result in further improvements of this breeding pool.

The remarkable morphological diversity of leaf shape in sweet potato (Ipomoea batatas): the influence of genetics, environment, and G×E

Leaf shape, a spectacularly diverse plant trait, varies across taxonomic levels, geography and in response to environmental differences. However, comprehensive intraspecific analyses of leaf shape variation across variable environments is surprisingly absent. Here, we performed a multilevel analysis of leaf shape using diverse accessions of sweet potato (Ipomoea batatas), and uncovered the role of genetics, environment, and G×E on this important trait. We examined leaf shape using a variety of morphometric analyses, and complement this with a transcriptomic survey to identify gene expression changes associated with shape variation. Additionally, we examined the role of genetics and environment on leaf shape by performing field studies in two geographically separate common gardens. We showed that extensive leaf shape variation exists within I. batatas, and identified promising candidate genes associated with this variation. Interestingly, when considering traditional measures, we found that genetic factors are largely responsible for most of leaf shape variation, but that the environment is highly influential when using more quantitative measures via leaf outlines. This extensive and multilevel examination of leaf shape shows an important role of genetics underlying a potentially important agronomic trait, and highlights that the environment can be a strong influence when using more quantitative measures of leaf shape.

A framework for genomics-informed ecophysiological modeling in plants

Dynamic process-based plant models capture complex physiological response across time, carrying the potential to extend simulations out to novel environments and lend mechanistic insight to observed phenotypes. Despite the translational opportunities for varietal crop improvement that could be unlocked by linking natural genetic variation to first principles-based modeling, these models are challenging to apply to large populations of related individuals. Here we use a combination of model development, experimental evaluation, and genomic prediction in Brassica rapa L. to set the stage for future large-scale process-based modeling of intraspecific variation. We develop a new canopy growth submodel for B. rapa within the process-based model Terrestrial Regional Ecosystem Exchange Simulator (TREES), test input parameters for feasibility of direct estimation with observed phenotypes across cultivated morphotypes and indirect estimation using genomic prediction on a recombinant inbred line population, and explore model performance on an in silico population under non-stressed and mild water-stressed conditions. We find evidence that the updated whole-plant model has the capacity to distill genotype by environment interaction (G×E) into tractable components. The framework presented offers a means to link genetic variation with environment-modulated plant response and serves as a stepping stone towards large-scale prediction of unphenotyped, genetically related individuals under untested environmental scenarios.

Modeling Interaction and Dispersion Effects in the Analysis of Gene-by-Environment Interaction

Genotype-by-environment interaction (GxE) studies probe heterogeneity in response to risk factors or interventions. Popular methods for estimation of GxE examine multiplicative interactions between individual genetic and environmental measures. However, risk factors and interventions may modulate the total variance of an epidemiological outcome that itself represents the aggregation of many other etiological components. We expand the traditional GxE model to directly model genetic and environmental moderation of the dispersion of the outcome. We derive a test statistic, [Formula: see text], for inferring whether an interaction identified between individual genetic and environmental measures represents a more general pattern of moderation of the total variance in the phenotype by either the genetic or the environmental measure. We validate our method via extensive simulation, and apply it to investigate genotype-by-birth year interactions for Body Mass Index (BMI) with polygenic scores in the Health and Retirement Study (N = 11,586) and individual genetic variants in the UK Biobank (N = 380,605). We find that changes in the penetrance of a genome-wide polygenic score for BMI across birth year are partly representative of a more general pattern of expanding BMI variation across generations. Three individual variants found to be more strongly associated with BMI among later born individuals, were also associated with the magnitude of variability in BMI itself within any given birth year, suggesting that they may confer general sensitivity of BMI to a range of unmeasured factors beyond those captured by birth year. We introduce an expanded GxE regression model that explicitly models genetic and environmental moderation of the dispersion of the outcome under study. This approach can determine whether GxE interactions identified are specific to the measured predictors or represent a more general pattern of moderation of the total variance in the outcome by the genetic and environmental measures.

Contemporary Modeling of Gene × Environment Effects in Randomized Multivariate Longitudinal Studies

There is a great deal of interest in the analysis of Genotype × Environment interactions (G×E). There are some limitations in the typical models for the analysis of G×E, including well-known statistical problems in identifying interactions and unobserved heterogeneity of persons across groups. The impact of a treatment may depend on the level of an unobserved variable, and this variation may dampen the estimated impact of treatment. Some researchers have noted that genetic variation may sometimes account for unobserved, and hence unaccounted for, heterogeneity. The statistical power associated with the G×E design has been studied in many different ways, and most results show that the small effects expected require relatively large or nonrepresentative samples (i.e., extreme groups). In this article, we describe some alternative approaches, such as randomized designs with multiple measures, multiple groups, multiple occasions, and analyses, to identify latent (unobserved) classes of people. These approaches are illustrated with data from the Aging, Demographics, and Memory Study (part of the Health and Retirement Study) examining the relations among episodic memory (based on word recall), APOE4 genotype, and educational attainment (as a proxy for an environmental exposure). Randomized clinical trials (RCTs) and randomized field trials (RFTs) have multiple strengths in the estimation of causal influences, and we discuss how measured genotypes can be incorporated into these designs. Use of these contemporary modeling techniques often requires different kinds of data be collected and encourages the formation of parsimonious models with fewer overall parameters, allowing specific G×E hypotheses to be investigated with a reasonable statistical foundation.

Adaptive developmental plasticity in rhesus macaques: the serotonin transporter gene interacts with maternal care to affect juvenile social behaviour

Research has increasingly highlighted the role that developmental plasticity-the ability of a particular genotype to produce variable phenotypes in response to different early environments-plays as an adaptive mechanism. One of the most widely studied genetic contributors to developmental plasticity in humans and rhesus macaques is a serotonin transporter gene-linked polymorphic region (5-HTTLPR), which determines transcriptional efficiency of the serotonin transporter gene in vitro and modifies the availability of synaptic serotonin in these species. A majority of studies to date have shown that carriers of a loss-of-function variant of the 5-HTTLPR, the short (s) allele, develop a stress-reactive phenotype in response to adverse early environments compared with long (l) allele homozygotes, leading to the prevalent conceptualization of the s-allele as a vulnerability allele. However, this framework fails to address the independent evolution of these loss-of-function mutations in both humans and macaques as well as the high population prevalence of s-alleles in both species. Here we show in free-ranging rhesus macaques that s-allele carriers benefit more from supportive early social environments than l-allele homozygotes, such that s-allele carriers which receive higher levels of maternal protection during infancy demonstrate greater social competence later in life. These findings provide, to our knowledge, the first empirical support for the assertion that the s-allele grants high undirected biological sensitivity to context in primates and suggest a mechanism through which the 5-HTTLPR s-allele is maintained in primate populations.

Efficient generalized least squares method for mixed population and family-based samples in genome-wide association studies

Genome-wide association studies (GWAS) that draw samples from multiple studies with a mixture of relationship structures are becoming more common. Analytical methods exist for using mixed-sample data, but few methods have been proposed for the analysis of genotype-by-environment (G×E) interactions. Using GWAS data from a study of sarcoidosis susceptibility genes in related and unrelated African Americans, we explored the current analytic options for genotype association testing in studies using both unrelated and family-based designs. We propose a novel method-generalized least squares (GLX)-to estimate both SNP and G×E interaction effects for categorical environmental covariates and compared this method to generalized estimating equations (GEE), logistic regression, the Cochran-Armitage trend test, and the WQLS and MQLS methods. We used simulation to demonstrate that the GLX method reduces type I error under a variety of pedigree structures. We also demonstrate its superior power to detect SNP effects while offering computational advantages and comparable power to detect G×E interactions versus GEE. Using this method, we found two novel SNPs that demonstrate a significant genome-wide interaction with insecticide exposure-rs10499003 and rs7745248, located in the intronic and 3' UTR regions of the FUT9 gene on chromosome 6q16.1.

Interaction between childhood adversity and functional polymorphisms in the dopamine pathway on first-episode psychosis

BACKGROUND

There is consistent evidence of a cumulative relationship between childhood adversity and psychosis, with number of adversities experienced increasing the probability of psychosis onset. It is possible that genetic factors moderate the association between childhood adversity and psychosis, potentially by influencing how an individual reacts biologically and/or psychologically following exposure to adversity, in such a way as to set them off on the path to psychosis. However, identifying the specific genetic variants involved and how they interact with childhood adversity remains challenging. We examined whether the association between cumulative exposure to childhood adversity and development of psychotic disorder was moderated by the COMT Val¹⁵⁸Met, AKT1 rs2494732 or DRD2 rs1076560 polymorphisms, known to affect dopamine levels.

METHODS

Participants were 285 first-presentation psychosis cases and 256 geographically-matched controls drawn from the Genetics and Psychosis (GAP) study. Childhood adversity was assessed using the Childhood Experience of Care and Abuse Questionnaire (CECA.Q) and blood- and cheek-derived genotype data were collected.

RESULTS

Our findings revealed no main effect of COMT Val¹⁵⁸Met, AKT1 rs2494732 and DRD2 rs1076560 polymorphisms on psychosis case status or reports of childhood adversity. Individuals reporting a history of multiple adversities were more likely to be psychosis patients than controls, regardless of their genetic risk. There was no evidence of candidate genotype by childhood adversity interactions in relation to psychosis onset.

CONCLUSION

These findings did not provide evidence of a possible role of COMT Val¹⁵⁸Met, AKT1 rs2494732 or DRD2 rs1076560 genotypes in modifying the association between childhood adversity and onset of psychosis.

Plasticity and genetic variation in traits underpinning asexual replication of the rodent malaria parasite, Plasmodium chabaudi

BACKGROUND

The ability of malaria (Plasmodium) parasites to adjust investment into sexual transmission stages versus asexually replicating stages is well known, but plasticity in other traits underpinning the replication rate of asexual stages in the blood has received less attention. Such traits include burst size (the number of merozoites produced per schizont), the duration of the asexual cycle, and invasion preference for different ages of red blood cell (RBC).

METHODS

Here, plasticity [environment (E) effects] and genetic variation [genotype (G) effects] in traits relating to asexual replication rate are examined for 4 genotypes of the rodent malaria parasite Plasmodium chabaudi. An experiment tested whether asexual dynamics differ between parasites infecting control versus anaemic hosts, and whether variation in replication rate can be explained by differences in burst size, asexual cycle, and invasion rates.

RESULTS

The within-host environment affected each trait to different extents but generally had similar impacts across genotypes. The dynamics of asexual densities exhibited a genotype by environment effect (G×E), in which one of the genotypes increased replication rate more than the others in anaemic hosts. Burst size and cycle duration varied between the genotypes (G), while burst size increased and cycle duration became longer in anaemic hosts (E). Variation in invasion rates of differently aged RBCs was not explained by environmental or genetic effects. Plasticity in burst size and genotype are the only traits making significant contributions to the increase in asexual densities observed in anaemic hosts, together explaining 46.4% of the variation in replication rate.

CONCLUSIONS

That host anaemia induces several species of malaria parasites to alter conversion rate is well documented. Here, previously unknown plasticity in other traits underpinning asexual replication is revealed. These findings contribute to mounting evidence that malaria parasites deploy a suite of sophisticated strategies to maximize fitness by coping with, or exploiting the opportunities provided by, the variable within-host conditions experienced during infections. That genetic variation and genotype by environment interactions also shape these traits highlights their evolutionary potential. Asexual replication rate is a major determinant of virulence and so, understanding the evolution of virulence requires knowledge of the ecological (within-host environment) and genetic drivers of variation among parasites.

Depressive symptoms in adolescence: The role of perceived parental support, psychological control, and proactive control in interaction with 5-HTTLPR

BACKGROUND

Parenting dimensions are associated with depressive symptoms in adolescents. We investigated the role of perceived parenting dimensions and gene-environment interactions between these perceived parenting dimensions and five well-known variable number of tandem repeats (VNTRs): 5-HTTLPR, STin2, DAT1, DRD4, and MAO-A, in depressive symptoms.

METHODS

From a non-clinical sample of 1111 Belgian adolescents (mean age: 13.79 years, SD=.94; 51% boys), 1103 adolescents consented for genetic research. Five VNTRs were analyzed using DNA from saliva samples. Perceived parenting dimensions (i.e., support, proactive control, psychological control, punishment, and harsh punishment) were examined using self-report scales completed by adolescents and their parents. Depressive symptoms were investigated using the CES-D self-report scale. Statistical analyses were performed in R using linear regression.

RESULTS

Parental support, as perceived by the adolescent, was negatively associated with depressive symptoms (CES-D) and psychological control was positively associated with these symptoms. The only interaction effect withstanding correction for multiple testing was observed for 5-HTTLPR and the difference in proactive control as perceived by adolescents in comparison to parents. Short-allele carriers showed more depressive symptoms when there was a higher discrepancy in proactive control as perceived by adolescents versus parents.

CONCLUSIONS

Our results suggest that perceived parenting dimensions are associated with depressive symptoms, as measured by the CES-D. We only found modest evidence for 5-HTTLPR as a moderator in the association between the difference in perception of proactive control (adolescents vs. parents) and depressive symptoms.

The Genetic, Environmental, and Cultural Forces Influencing Youth Antisocial Behavior Are Tightly Intertwined

The aggressive and rule-breaking behaviors that constitute youth antisocial behavior (ASB) are shaped by intertwined genetic, developmental, familial, spatial, temporal, cultural, interpersonal, and contextual influences operating across multiple levels of analysis. Genetic influences on ASB, for example, manifest in different ways during different developmental periods, and do so in part as a function of exposure to harsh parenting, delinquent peers, and disadvantaged neighborhoods. There is also clear evidence documenting societal effects, time-period effects, sex-assigned-at-birth effects, and cohort effects, all of which point to prominent (and possibly interconnected) cultural influences on ASB. In short, ASB is shaped by individuals' current and prior environmental experiences, genetic risks, and the time and place in which they live. This review seeks to illuminate already documented instances of interplay among the multilevel etiologic forces impinging on youth ASB, with the goal of facilitating additional research.

Romantic Relationship Satisfaction Moderates the Etiology of Adult Personality

The heritability of major normative domains of personality is well-established, with approximately half the proportion of variance attributed to genetic differences. In the current study, we examine the possibility of gene × environment interaction (G×E) for adult personality using the environmental context of intimate romantic relationship functioning. Personality and relationship satisfaction are significantly correlated phenotypically, but to date no research has examined how the genetic and environmental components of variance for personality differ as a function of romantic relationship satisfaction. Given the importance of personality for myriad outcomes from work productivity to psychopathology, it is vital to identify variables present in adulthood that may affect the etiology of personality. In the current study, quantitative models of G×E were used to determine whether the genetic and environmental influences on personality differ as a function of relationship satisfaction. We drew from a sample of now-adult twins followed longitudinally from adolescence through age 29. All participants completed the Multidimensional Personality Questionnaire (MPQ) and an abbreviated version of the Dyadic Adjustment Scale. Biometric moderation was found for eight of the eleven MPQ scales examined: well-being, social potency, negative emotionality, alienation, aggression, constraint, traditionalism, and absorption. The pattern of findings differed, suggesting that the ways in which relationship quality moderates the etiology of personality may depend on the personality trait.

Implementation of Epigenetic Variation in Sorghum Selection and Implications for Crop Resilience Breeding

Crop resilience and yield stability are complex traits essential for food security. Sorghum bicolor is an important grain crop that shows promise for its natural resilience to drought and potential for marginal land production. We have developed sorghum lines in the Tx430 genetic background suppressed for MSH1 expression as a means of inducing de novo epigenetic variation, and have used these materials to evaluate changes in plant growth vigor. Plant crossing and selection in two distinct environments revealed features of phenotypic plasticity derived from MSH1 manipulation. Introduction of an epigenetic variation to an isogenic sorghum population, in the absence of selection, resulted in 10% yield increase under ideal field conditions and 20% increase under extreme low nitrogen conditions. However, incorporation of early-stage selection amplified these outcomes to 36% yield increase under ideal conditions and 64% increase under marginal field conditions. Interestingly, the best outcomes were derived by selecting mid-range performance early-generation lines rather than highest performing. Data also suggested that phenotypic plasticity derived from the epigenetic variation was non-uniform in its response to environmental variability but served to reduce genotype × environment interaction. The MSH1-derived growth vigor appeared to be associated with enhanced seedling root growth and altered expression of auxin response pathways, and plants showed evidence of cold tolerance, features consistent with observations made previously in Arabidopsis. These data imply that the MSH1 system is conserved across plant species, pointing to the value of parallel model plant studies to help devise effective plant selection strategies for epigenetic breeding in multiple crops.

Latitudinal clines in bud flush phenology reflect genetic variation in chilling requirements in balsam poplar, Populus balsamifera

PREMISE

Boreal and northern temperate forest trees possess finely tuned mechanisms of dormancy, which match bud phenology with local seasonality. After winter dormancy, the accumulation of chilling degree days (CDD) required for rest completion before the accumulation of growing degree days (GDD) during quiescence is an important step in the transition to spring bud flush. While bud flush timing is known to be genetically variable within species, few studies have investigated variation among genotypes from different climates in response to variable chilling duration.

METHODS

We performed a controlled environment study using dormant cuttings from 10 genotypes of Populus balsamifera, representing a broad latitudinal gradient (43-58°N). We exposed cuttings to varying amounts of chilling (0-10 weeks) and monitored subsequent GDD to bud flush at a constant forcing temperature.

RESULTS

Chilling duration strongly accelerated bud flush timing, with increasing CDD resulting in fewer GDD to flush. Genotypic variation for bud flush was significant and stratified by latitude, with southern genotypes requiring more GDD to flush than northern genotypes. The latitudinal cline was pronounced under minimal chilling, whereas genotypic variation in GDD to bud flush converged as CDD increased.

CONCLUSIONS

We demonstrate that increased chilling lessens GDD to bud flush in a genotype-specific manner. Our results emphasize that latitudinal clines in bud flush reflect a critical genotype-by-environment interaction, whereby differences in bud flush between southern vs. northern genotypes depend on chilling. Our results suggest selection has shaped chilling requirements and depth of rest as an adaptive strategy to avoid precocious flush in climates with midwinter warming.

Environment-specific selection alters flowering-time plasticity and results in pervasive pleiotropic responses in maize

Crop genetic diversity for climate adaptations is globally partitioned. We performed experimental evolution in maize to understand the response to selection and how plant germplasm can be moved across geographical zones. Initialized with a common population of tropical origin, artificial selection on flowering time was performed for two generations at eight field sites spanning 25° latitude, a 2800 km transect. We then jointly tested all selection lineages across the original sites of selection, for the target trait and 23 other traits. Modeling intergenerational shifts in a physiological reaction norm revealed separate components for flowering-time plasticity. Generalized and local modes of selection altered the plasticity of each lineage, leading to a latitudinal pattern in the responses to selection that were strongly driven by photoperiod. This transformation led to widespread changes in developmental, architectural, and yield traits, expressed collectively in an environment-dependent manner. Furthermore, selection for flowering time alone alleviated a maladaptive syndrome and improved yields for tropical maize in the temperate zone. Our findings show how phenotypic selection can rapidly shift the flowering phenology and plasticity of maize. They also demonstrate that selecting crops to local conditions can accelerate adaptation to climate change.

Remote sensing of cytotype and its consequences for canopy damage in quaking aspen

Mapping geographic mosaics of genetic variation and their consequences via genotype x environment interactions at large extents and high resolution has been limited by the scalability of DNA sequencing. Here, we address this challenge for cytotype (chromosome copy number) variation in quaking aspen, a drought-impacted foundation tree species. We integrate airborne imaging spectroscopy data with ground-based DNA sequencing data and canopy damage data in 391 km² of southwestern Colorado. We show that (1) aspen cover and cytotype can be remotely sensed at 1 m spatial resolution, (2) the geographic mosaic of cytotypes is heterogeneous and interdigitated, (3) triploids have higher leaf nitrogen, canopy water content, and carbon isotope shifts (δ¹³ C) than diploids, and (4) canopy damage varies among cytotypes and depends on interactions with topography, canopy height, and trait variables. Triploids are at higher risk in hotter and drier conditions.

Deciphering transcriptomic signatures explaining the phenotypic plasticity of nonheading lettuce genotypes under artificial light conditions

Elucidating the mechanisms and pathways involved in genotype-environment (G×E) interactions and phenotypic plasticity is critical for improving plant growth. Controlled environment agricultural systems allow growers to modulate the environment for particular genotypes. In this study, we evaluated the effects of interactions among 14 genotypes and four artificial light environments on leaf lettuce phenotypes and dissected the underlying molecular mechanism via transcriptome-based modeling. Variations in morphological traits and phytochemical concentrations in response to artificial light treatments revealed significant G×E interactions. The appropriate genotype and artificial light combinations for maximizing phenotypic expression were determined on the basis of a joint regression analysis and the additive main effect and multiplicative interaction model for these G×E interactions. Transcriptome-based regression modeling explained approximately 50%-90% of the G×E variations. Further analyzes indicated Red Lettuce Leaves 4 (RLL4) regulates UV-B and blue light signaling through the effects of the HY5-MBW pathway on flavonoid biosynthesis and contributes to natural variations in the light-responsive plasticity of lettuce traits. Our study represents an important step toward elucidating the phenotypic variations due to G×E interactions in nonheading lettuce under artificial light conditions.

Interactions between Genetic, Prenatal, Cortisol, and Parenting Influences on Adolescent Substance Use and Frequency: A TRAILS Study

INTRODUCTION

Dynamic relations between genetic, hormone, and pre- and postnatal environments are theorized as critically important for adolescent substance use but are rarely tested in multifactorial models. This study assessed the impact of interactions of genetic risk and cortisol reactivity with prenatal and parenting influences on both any and frequency of adolescent substance use.

METHODS

Data are from the TRacking Adolescents' Individual Lives Survey (TRAILS), a prospective longitudinal, multi-rater study of 2,230 Dutch adolescents. Genetic risk was assessed via 3 substance-specific polygenic scores. Mothers retrospectively reported prenatal risk when adolescents were 11 years old. Adolescents rated their parents' warmth and hostility at age 11. Salivary cortisol reactivity was measured in response to a social stress task at age 16. Adolescents' self-reported cigarette, alcohol, and cannabis use frequency at age 16.

RESULTS

A multivariate hurdle regression model showed that polygenic risk for smoking, alcohol, and cannabis predicted any use of each substance, respectively, but predicted more frequent use only for smoking. Blunted cortisol reactivity predicted any use and more frequent use for all 3 outcomes. There were 2 interactions: blunted cortisol reactivity exacerbated the association of polygenic risk with any smoking and the association of prenatal risk with any alcohol use.

CONCLUSION

Polygenic risk seems of importance for early use but less so for frequency of use, whereas blunted cortisol reactivity was correlated with both. Blunted cortisol reactivity may also catalyze early risks for substance use, though to a limited degree. Gene-environment interactions play no role in the context of this multifactorial model.