Additive and Interactive Associations of Environmental and Sociodemographic Factors with the Genotypes of Three Glutathione S-Transferase Genes in Relation to the Blood Arsenic Concentrations of Children in Jamaica

Arsenic (As) is a metalloid that has been classified as a xenobiotic with toxic effects on human beings, especially on children. Since the soil in Jamaica contains As, dietary intake is considered the main source of As exposure in Jamaicans. In addition, glutathione S-transferase (GST) genes, including GSTT1, GSTP1, and GSTM1, play an important role in the metabolism of xenobiotics including As in humans. Using data from 375 typically developing children (2–8 years) in Jamaica, we investigated the environmental and sociodemographic factors, as well as their possible interactions with the children’s genotype for GST genes in relation to having a detectable level of blood As concentration (i.e., >1.3 μg/L). Using multivariable logistic regression, we have identified environmental factors significantly associated with blood As concentrations that include a child’s age, parental education levels, and the consumption of saltwater fish, cabbage, broad beans, and avocado (all p < 0.01). Based on the multivariable analysis including gene x environment interactions, we found that among children with the Ile/Ile genotype for GSTP1 Ile105Val, children who consumed avocado had higher odds of having a detectable blood As concentration compared to children who did not eat avocado.

TREND, POPULATION STRUCTURE AND TRAIT MAPPING FROM 15 YEARS OF NATIONAL VARIETAL TRIALS OF UK WINTER WHEAT

There are now a rich variety of genomic and genotypic resources available to wheat researchers and breeders. However, the generation of high-quality and field-relevant phenotyping data which is required to capture the complexities of gene x environment interactions remains a major bottleneck. Historical datasets from national variety performance trials (NVPT) provide sufficient dimensions, in terms of numbers of years and locations, to examine phenotypic trends and study gene x environment interactions. Using NVPT for winter wheat varieties grown in the UK between 2002 – 2017, we examined temporal trends for eight traits related to yield, adaptation, and grain quality performance. We show a non-stationary linear trend for yield, grain protein content, HFN and days to ripening. Our data also show high environmental stability for yield, grain protein content and specific weight in UK winter wheat varieties and high environmental sensitivity for Hagberg Falling Number. We also show that UK varieties released within this period cluster into four main population groups. Using the historical NVPT data in a genome-wide association analysis, we uncovered a significant marker-trait association peak on wheat chromosome 6A spanning the NAM-A1 gene that have been previously associated with early senescence. Together our results show the value of utilizing the data routinely collected during national variety evaluation process for examining breeding progress and the genetic architecture of important traits.

Trend, Population Structure And Trait Mapping From 15 Years Of National Varietal Trials Of UK Winter Wheat

There are now a rich variety of genomic and genotypic resources available to wheat researchers and breeders. However, the generation of high-quality and field-relevant phenotyping data which is required to capture the complexities of gene x environment interactions remains a major bottleneck. Historical datasets from national variety performance trials (NVPT) provide sufficient dimensions, in terms of numbers of years and locations, to examine phenotypic trends and study gene x environment interactions. Using NVPT for winter wheat varieties grown in the UK between 2002 – 2017, we examined temporal trends for eight traits related to yield, adaptation, and grain quality performance. We show a non-stationary linear trend for yield, grain protein content, HFN and days to ripening. Our data also show high environmental stability for yield, grain protein content and specific weight in UK winter wheat varieties and high environmental sensitivity for Hagberg Falling Number. Using the historical NVPT data in a genome-wide association analysis, we uncovered a significant marker-trait association peak on wheat chromosome 6A spanning the NAM-A1 gene that have been previously associated with early senescence. Together our results show the value of utilizing the data routinely collected during variety evaluation process for examining breeding progress and the genetic architecture of important traits.

Interactions of Genetic and Environment Scores: Alternating Lasso Regularization Avoids Overfitting and Finds Interpretable Scores

Regression models with interaction terms are common models for moderating relationships. When several predictors from one group, e.g., genetic variables, are potentially moderated by several predictors from another, e.g., environmental variables, many interaction terms result. This complicates model interpretation, especially when coefficient signs point in different directions. By first forming a score for each group of predictors, the interaction model's dimension is severely reduced. The hierarchical score model is an elegant one step approach: Score weights and regression model coefficients are estimated simultaneously by an alternating optimization (AO) algorithm. Especially in high dimensional settings, scores remain an effective technique to reduce interaction model dimension, and we propose regularization to ensure sparsity and interpretability of the score weights. A non-trivial extension of the original AO algorithm is presented, which adds a lasso penalty, resulting in the alternating lasso optimization algorithm (ALOA). The hierarchical score model with ALOA is an interpretable statistical learning technique for moderation in potentially high dimensional applications, and encompasses generalized linear models for the main interaction model. In addition to the lasso regularization, a screening procedure called regularization and residualization (RR) is proposed to avoid spurious interactions. ALOA tuning parameter choice and the RR screening procedure are investigated by simulations, and an illustrative application to lifetime depression risk and gene x environment interactions is provided.

Genetics and Genomics of Pediatric Pulmonary Arterial Hypertension

Pulmonary arterial hypertension is a rare disease with high mortality despite recent therapeutic advances. The disease is caused by both genetic and environmental factors, and likely gene x environment interactions. While PAH can manifest across the lifespan, pediatric-onset disease is particularly challenging because it is frequently associated with a more severe clinical course and comorbidities including lung/heart developmental anomalies. In light of these differences, it is perhaps not surprising that emerging data from genetic studies of pediatric-onset PAH indicate that the genetic basis is different than that of adults. There is a greater genetic burden in children, with rare genetic factors contributing to at least 36% of pediatric-onset idiopathic PAH (IPAH) compared to ~11% of adult-onset IPAH. De novo variants are frequently associated with PAH in children, and contribute to at least 15% of all pediatric cases. The standard of medical care for pediatric PAH patients is based on extrapolations from adult data. However, the increased etiologic heterogeneity, poorer prognosis and increased genetic burden for pediatric-onset PAH calls for a dedicated pediatric research agenda to improve molecular diagnosis and clinical management. A genomics-first approach will improve the understanding of pediatric PAH and how it is related to other rare pediatric genetic disorders.

Photoperiodic Effects on Monoamine Signaling & Gene Expression Throughout Development in the Serotonin & Dopamine Systems

Photoperiod or the duration of daylight has been implicated as a risk factor in the development of mood disorders. The dopamine and serotonin systems are impacted by photoperiod and are consistently associated with affective disorders. Hence, we evaluated, at multiple stages of postnatal development, the expression of key dopaminergic (TH) and serotonergic (Tph2, SERT, and Pet-1) genes, and midbrain monoamine content in mice raised under control Equinox (LD 12:12), Short winter-like (LD 8:16), or Long summerlike (LD 16:8) photoperiods. Focusing in early adulthood, we evaluated the midbrain levels of these serotonergic genes, and also assayed these gene levels in the dorsal raphe nucleus (DRN) with RNAScope. Mice that developed under Short photoperiods demonstrated elevated midbrain TH expression levels, specifically during perinatal development compared to mice raised under Long photoperiods, and significantly decreased serotonin and dopamine content throughout the course of development. In adulthood, Long photoperiod mice demonstrated decreased midbrain Tph2 and SERT expression levels and reduced Tph2 levels in the DRN compared Short photoperiod mice. Thus, evaluating gene x environment interactions in the dopaminergic and serotonergic systems during multiple stages of development may lead to novel insights into the underlying mechanisms in the development of affective disorders.