Significant Heritability Research Articles

The individuality of shape asymmetries of the human cerebral cortex.

Asymmetries of the cerebral cortex are found across diverse phyla and are particularly pronounced in humans, with important implications for brain function and disease. However, many prior studies have confounded asymmetries due to size with those due to shape. Here, we introduce a novel approach to characterize asymmetries of the whole cortical shape, independent of size, across different spatial frequencies using magnetic resonance imaging data in three independent datasets. We find that cortical shape asymmetry is highly individualized and robust, akin to a cortical fingerprint, and identifies individuals more accurately than size-based descriptors, such as cortical thickness and surface area, or measures of inter-regional functional coupling of brain activity. Individual identifiability is optimal at coarse spatial scales (~37 mm wavelength), and shape asymmetries show scale-specific associations with sex and cognition, but not handedness. While unihemispheric cortical shape shows significant heritability at coarse scales (~65 mm wavelength), shape asymmetries are determined primarily by subject-specific environmental effects. Thus, coarse-scale shape asymmetries are highly personalized, sexually dimorphic, linked to individual differences in cognition, and are primarily driven by stochastic environmental influences.

Methods for estimation of genetic parameters in soybeans: an alternative to adjust residual variability

Selection practices are maximized when plant breeders have the availability of consolidated parameters, which will guide direct and indirect selection methods. This study aimed to apply a biometric alternative to minimize residual variance and maximize selection parameters by parent-progeny regression, interim controls, and mixed linear models intrinsic to breeding. The obtained data were subjected to the assumptions of the statistical model, which identified the normality and homogeneity of the residual variances and model additivity. Subsequently, two analysis scenarios were created. The first preserved all information obtained in the experiment, both from segregating families and pure-line cultivars, and was called original scenario. The other scenario preserved progeny data, but the residual variability of controls was restricted using as criterion observations contained between the interval of the first sample standard deviation. Thereby, an acceptable residue limit could be obtained. Both scenarios were submitted to three consolidated frequentist methods (genitor-progeny regression; sum of squares of augmented block design with interim controls; and mixed linear models, wherein random genetic effects are taken as weighted genetic parameters by the genealogical matrix). Restricting residual variation in parents or controls can maximize genetic parameters and genetic gains in soybean breeding. Significant heritability estimate gains were obtained in the augmented blocks with interim control approach. Mixed linear models with random genetic effects can be considered a great tool to obtain genetic parameters in experiments with a high magnitude of common and regular treatments.

Identification of genetic loci shared between Alzheimer's disease and hypertension.

Alzheimer's disease (AD) and high blood pressure (BP) are prevalent age-related diseases with significant unexplained heritability. A thorough analysis of genetic pleiotropy between AD and BP will lay a foundation for the study of the associated molecular mechanisms, leading to a better understanding of the development of each phenotype. We used the conditional false discovery rate (cFDR) method to identify novel genetic loci associated with both AD and BP. The cFDR approach improves the effective sample size for association testing by combining GWAS summary statistics for correlated phenotypes. We identified 50 pleiotropic SNPs for AD and BP, 7 of which are novel and have not previously been reported to be associated with either AD or BP. The novel SNPs located at STK3 are particularly noteworthy, as this gene may influence AD risk via the Hippo signaling network, which regulates cell death. Bayesian colocalization analysis demonstrated that although AD and BP are associated, they do not appear to share the same causal variants. We further performed two sample Mendelian randomization analysis, but could not detect a causal effect of BP on AD. Despite the inability to establish a causal link between AD and BP, our findings report some potential novel pleiotropic loci that may influence disease susceptibility. In summary, we identified 7 SNPs that annotate to 4 novel genes which have not previously been reported to be associated with AD nor with BP and discuss the possible role of one of these genes, STK3 in the Hippo signaling network.

Assessment of Genetic Variability Parameters and Character Association in Chickpea (Cicer arietinum L.)

School of Agriculture, ITM University in Gwalior's Department of Genetics and Plant Breeding performed a Rabi season 2021–2022 study on 15 distinct genotypes of chickpeas to better understand their genetic variability. The genotypes were distributed using a Randomized Block Design with three replications. On the plants themselves, data was gathered on their overall height, the number of main and secondary branches they had at 50% flowering, the number of pods and seeds they had at 100 seeds weight, days to maturity, as well as their grain yields per plant and the total yield per plot. After analyzing the data, A statistical study of each character's genotypes revealed a wide range of results. Plant height, number of main and secondary branches, days to 50% flowering, days to maturity, number of pods per plant, and 100 seed weight provided the highest GCV and PCV values in the experiment. All of these traits, as well as plant height, secondary branch count, days until 50% of the flowers open, pod count per plant, grain production per plant, and total yield per plot, demonstrated significant heritability and genetic advancement as a percentage of the mean. Traits such as plant height, no of seeds per pod, and total yield per plot, exhibited a significant positive correlation with grain yield per plant and this will show a greater direct effect on single yield plant.

Machine learning of large-scale multimodal brain imaging data reveals neural correlates of hand preference

Lateralization is a fundamental characteristic of many behaviors and the organization of the brain, and atypical lateralization has been suggested to be linked to various brain-related disorders such as autism and schizophrenia. Right-handedness is one of the most prominent markers of human behavioural lateralization, yet its neurobiological basis remains to be determined. Here, we present a large-scale analysis of handedness, as measured by self-reported direction of hand preference, and its variability related to brain structural and functional organization in the UK Biobank (N = 36,024). A multivariate machine learning approach with multi-modalities of brain imaging data was adopted, to reveal how well brain imaging features could predict individual's handedness (i.e., right-handedness vs. non-right-handedness) and further identify the top brain signatures that contributed to the prediction. Overall, the results showed a good prediction performance, with an area under the receiver operating characteristic curve (AUROC) score of up to 0.72, driven largely by resting-state functional measures. Virtual lesion analysis and large-scale decoding analysis suggested that the brain networks with the highest importance in the prediction showed functional relevance to hand movement and several higher-level cognitive functions including language, arithmetic, and social interaction. Genetic analyses of contributions of common DNA polymorphisms to the imaging-derived handedness prediction score showed a significant heritability (h2=7.55%, p <0.001) that was similar to and slightly higher than that for the behavioural measure itself (h2=6.74%, p <0.001). The genetic correlation between the two was high (rg=0.71), suggesting that the imaging-derived score could be used as a surrogate in genetic studies where the behavioural measure is not available. This large-scale study using multimodal brain imaging and multivariate machine learning has shed new light on the neural correlates of human handedness.

Heritability Analyses Uncover Shared Genetic Effects of Lung Function and Change over Time.

Genetic influence on lung functions has been identified in previous studies; however, the relative longitudinal effects of genetic factors and their interactions with smoking on lung function remain unclear. Here, we identified the longitudinal effects of genetic variants on lung function by determining single nucleotide polymorphism (SNP) heritability and genetic correlations, and by analyzing interactions with smoking. Subject-specific means and annual change rates were calculated for eight spirometric measures obtained from 6622 Korean adults aged 40–69 years every two years for 14 years, and their heritabilities were estimated separately. Statistically significant (p < 0.05) heritability for the subject-specific means of all spirometric measures (8~32%) and change rates of forced expiratory volume in 1 s to forced vital capacity ratio (FEV1/FVC; 16%) and post-bronchodilator FEV1/FVC (17%) were detected. Significant genetic correlations of the change rate with the subject-specific mean were observed for FEV1/FVC ( = 0.64) and post-bronchodilator FEV1/FVC ( = 0.47). Furthermore, post-bronchodilator FEV1/FVC showed significant heritability of SNP-by-smoking interaction ( = 0.4) for the annual change rate. The GWAS also detected genome-wide significant SNPs for FEV1 (rs4793538), FEV1/FVC (rs2704589, rs62201158, and rs9391733), and post-bronchodilator FEV1/FVC (rs2445936). We found statistically significant evidence of heritability role on the change in lung function, and this was shared with the effects on cross-sectional measurements. We also found some evidence of interaction with smoking for the change of lung function.

Relative contributions of the host genome, microbiome, and environment to the metabolic profile.

Metabolic syndrome is as a well-known risk factor for cardiovascular disease, which is associated with both genetic and environmental factors. Recently, the microbiome composition has been shown to affect the development of metabolic syndrome. Thus, it is expected that the complex interplay among host genetics, the microbiome, and environmental factors could affect metabolic syndrome. To evaluate the relative contributions of genetic, microbiome, and environmental factors to metabolic syndrome using statistical approaches. Data from the prospective Korean Association REsource project cohort (N = 8476) were used in this study, including single-nucleotide polymorphisms, phenotypes and lifestyle factors, and the urine-derived microbial composition. The effect of each data source on metabolic phenotypes was evaluated using a heritability estimation approach and a prediction model separately. We further experimented with various types of metagenomic relationship matrices to estimate the phenotypic variance explained by the microbiome. With the heritability estimation, five of the 11 metabolic phenotypes were significantly associated with metagenome-wide similarity. We found significant heritability for fasting glucose (4.8%), high-density lipoprotein cholesterol (4.9%), waist-hip ratio (7.7%), and waist circumference (5.6%). Microbiome compositions provided more accurate estimations than genetic factors for the same sample size. In the prediction model, the contribution of each source to the prediction accuracy varied for each phenotype. The effects of host genetics, the metagenome, and environmental factors on metabolic syndrome were minimal. Our statistical analysis suffers from a small sample size, and the measurement error is expected to be substantial. Further analysis is necessary to quantify the effects with better accuracy.

HTR1B genotype and psychopathy: Main effect and interaction with paternal maltreatment

Psychopathy is a condition characterized by atypical emotions and socially maladaptive behavioral patterns. Among incarcerated people, psychopathy has been associated with higher rates of crimes, recidivism, and resistance to treatment. Many studies have indicated significant heritability of psychopathic traits, but little is known about the specific contribution of genes and their interaction with adverse experiences in life. Considering the primary role that serotonin plays in cognition and emotion, we investigated TPH2-rs4570625, 5-HTTLPR, MAOA-uVNTR, HTR1B-rs13212041 and HTR2A-rs6314 as risk factors for psychopathy in the largest sample of institutionalized individuals studied so far, consisting of 793 US White male incarcerated adults, and in a replication sample of 168 US White male incarcerated adolescents. In a subgroup of the adult sample, the interaction between genetics and parenting style, assessed by the Measure of Parental Style (MOPS) questionnaire, was also evaluated. The HTR1B-rs13212041-T/T genotype, as compared to HTR1B-rs13212041-C allele, predicted higher psychopathy scores in both the adult and the adolescent samples. The interaction between HTR1B-rs13212041-T/T genotype and paternal MOPS scores, investigated in a subgroup of the adult sample, was an even stronger predictor of higher levels of psychopathy than either the genetics or the environment taken individually. Overall, these data, obtained in two independent samples, shed new light on neurobiological correlates of psychopathy with promising implications both at a clinical and forensic level.

Evolution of hormone-phenotype couplings and hormone-genome interactions

When selection favors a new relationship between a cue and a hormonally mediated response, adaptation can proceed by altering the hormonal signal that is produced or by altering the phenotypic response to the hormonal signal. The field of evolutionary endocrinology has made considerable progress toward understanding the evolution of hormonal signals, but we know much less about the evolution of hormone-phenotype couplings, particularly at the hormone-genome interface. We briefly review and classify the mechanisms through which these hormone-phenotype couplings likely evolve, using androgens and their receptors and genomic response elements to illustrate our view. We then present two empirical studies of hormone-phenotype couplings, one rooted in evolutionary quantitative genetics and another in comparative transcriptomics, each focused on the regulation of sexually dimorphic phenotypes by testosterone (T) in the brown anole lizard (Anolis sagrei). First, we illustrate the potential for hormone-phenotype couplings to evolve by showing that coloration of the dewlap (an ornament used in behavioral displays) exhibits significant heritability in its responsiveness to T, implying that anoles harbor genetic variance in the architecture of hormonal pleiotropy. Second, we combine T manipulations with analyses of the liver transcriptome to ask whether and how statistical methods for characterizing modules of co-expressed genes and in silico techniques for identifying androgen response elements (AREs) can improve our understanding of hormone-genome interactions. We conclude by emphasizing important avenues for future work at the hormone-genome interface, particularly those conducted in a comparative evolutionary framework.

Nutritional compositions and functional properties of New Ethiopian chickpea varieties: Effects of variety, grown environment and season

ABSTRACT Chickpeas are nutritious legumes, which are a rich source of proteins, fiber, carbohydrate, vitamins and minerals. Factors affect the nutritional composition of crops including chickpeas like variety, growing environments and seasons are the most common. Studies have not yet reported on the effects of variety, grown location, and grown season on specifically for Ethiopia chickpea nutritional and functional characteristics. To address this, eleven released chickpea varieties were grown at three locations in Ethiopia, during 2018 and 2019 main cropping season, representing three different agroecological environments. Then functional properties, proximate and minerals composition and in chickpea flour were determined. Variation in most nutritional composition and functional properties of eleven chickpea varieties were observed among grown within each location in each season. Statistical analysis of combined data showed significant differences among varieties, locations, and grown season for each measured parameter. High proportion of the total variation for almost studied parameters explained by the main effects of variety indicates a significant heritability for them. Growing location was found to have a significant effect on all functional properties except OAC, total ash, crude fat, crude protein, carbohydrate, energy, calcium, magnesium, iron and zinc. Grown Season was found to affect OAC, WAC, SC, FS, EA, total ash, calcium, magnesium, iron and zinc. Rainfall is the climate characteristic that may be responsible for these year-dependent differences. HC and SC (r = 0.902) and energy and fat (r = 0.800) showed positive correlation whereas, carbohydrate and protein (r = −0.896) and energy and fiber (r = −0.674) showed negative correlation. The current study established a better understanding of the varietal effects of genotype and environment on functional and nutritional composition properties of chickpea flours.

Concurrent sodium channel myotonia and amyotrophic lateral sclerosis supports shared pathogenesis

Amyotrophic lateral sclerosis (ALS) is an invariably fatal adult-onset neurodegenerative disorder; 10% of ALS is autosomal dominant but even sporadic ALS exhibits significant heritability. Dysfunctional voltage- gated sodium channels (NaVs) have been implicated in both sporadic and familial forms of the disease, but it is unclear whether these are an upstream cause or a downstream consequence. Rare missense mutations in the SCN4A gene, encoding NaV1.4, disrupt membrane excitability and cause autosomal dominant muscle channelopathies such as myotonia and hypo/hyperkalaemic periodic paralysis. We report two patients with congenital SCN4A channelopathy due to p.S1159P and p.R672H mutations who developed ALS in later life. Based on our finding we hypothesised that ALS may be linked to genetic mutations in other voltage gated ion channels. Rare-variant burden testing using whole genome sequenc- ing data from 4,495 ALS patients and 1,925 controls within the superfamily of voltage-gated ion channels (Accession: ssf81324) identified one gene, SCN7A, which passed multiple testing correction (p=0.0002, Firth logistic regression) consistent with an enrichment of ALS-associated mutations. We propose that genetic mutations within NaVs leading to neuromuscular excitotoxicity are an upstream cause of ALS. Early identification of ALS patients carrying NaV mutations might lead to personalised therapy with a sodium channel-blocking agent such as riluzole.j.franklin@doctors.org.uk

Testing heritability of moral foundations: Common pathway models support strong heritability for the five moral foundations

Moral Foundations Theory (MFT) predicts that moral behaviour reflects at least five foundational traits, each hypothesised to be heritable. Here, we report two independent twin studies (total n = 2020), using multivariate multi-group common pathway models to test the following three predictions from the MFT: (1) The moral foundations will show significant heritability; (2) The moral foundations will each be genetically distinct and (3) The clustering of moral concerns around individualising and binding domains will show significant heritability. Supporting predictions 1 and 3, Study 1 showed evidence for significant heritability of two broad moral factors corresponding to individualising and binding domains. In Study 2, we added the second dataset, testing replication of the Study 1 model in a joint approach. This further corroborated evidence for heritable influence, showed strong influences on the individualising and binding domains (h2 = 49% and 66%, respectively) and, partially supporting prediction 2, showed foundation-specific, heritable influences on Harm/Care, Fairness/Reciprocity and Purity/Sanctity foundations. A general morality factor was required, also showing substantial genetic effects (40%). These findings indicate that moral foundations have significant genetic bases. These influenced the individual foundations themselves as well as a general concern for the individual, for the group, and overall moral concern.

Genetic analyses identify pleiotropy and causality for blood proteins and highlight Wnt/β-catenin signalling in migraine

Migraine is a common complex disorder with a significant polygenic SNP heritability ({h}_{{SNP}}^{2}). Here we utilise genome-wide association study (GWAS) summary statistics to study pleiotropy between blood proteins and migraine under the polygenic model. We estimate {h}_{{SNP}}^{2} for 4625 blood protein GWASs and identify 325 unique proteins with a significant {h}_{{SNP}}^{2} for use in subsequent genetic analyses. Pleiotropy analyses link 58 blood proteins to migraine risk at genome-wide, gene and/or single-nucleotide polymorphism levels—suggesting shared genetic influences or causal relationships. Notably, the identified proteins are largely distinct from migraine GWAS loci. We show that higher levels of DKK1 and PDGFB, and lower levels of FARS2, GSTA4 and CHIC2 proteins have a significant causal effect on migraine. The risk-increasing effect of DKK1 is particularly interesting—indicating a role for downregulation of β-catenin-dependent Wnt signalling in migraine risk, suggesting Wnt activators that restore Wnt/β-catenin signalling in brain could represent therapeutic tools against migraine.

Phenotypic and genetic associations between gray matter covariation and tool use skill in chimpanzees (Pan troglodytes): Repeatability in two genetically isolated populations

Humans and chimpanzees both exhibit a diverse set of tool use skills which suggests selection for tool manufacture and use occurred in the common ancestors of the two species. Our group has previously reported phenotypic and genetic associations between tool use skill and gray matter covariation, as quantified by source-based morphometry (SBM), in chimpanzees. As a follow up study, here we evaluated repeatability in heritability in SBM components and their phenotypic association with tool use skill in two genetically independent chimpanzee cohorts. Within the two independent cohorts of chimpanzees, we identified 8 and 16 SBM components, respectively. Significant heritability was evident for multiple SBM components within both cohorts. Further, phenotypic associations between tool use performance and the SBM components were largely consistent between the two cohorts; the most consistent finding being an association between tool use performance and an SBM component including the posterior superior temporal sulcus (STS) and superior temporal gyrus (STG), and the interior and superior parietal regions (p < 0.05). These findings indicate that the STS, STG, and parietal cortices are phenotypically and genetically implicated in chimpanzee tool use abilities.

Predictors of individual performance and evolutionary potential of life-history traits in a hematophagous ectoparasite.

Little is known about the intraspecific variation of parasite life‐history traits and how this variation may affect parasite fitness and evolution. We investigated how life‐history traits predict success of individual tree‐hole ticks Ixodes arboricola and estimated their evolutionary potential, as well as genetic correlations within stages and phenotypic correlations within and across stages. Ticks were followed individually over two generations while allowed to feed on great tits Parus major. After accounting for host and tick maternal effects, we found that short feeding times and high engorgement weights strongly increased molting success. Molting time was also positively correlated with feeding success in adults. In larvae and nymphs, we found negative phenotypic correlations between engorgement weight and both feeding and molting time, the latter supported by a negative genetic correlation. We found sex‐related differences in feeding time (longer in male nymphs) and molting time (longer in male larvae but shorter in male nymphs). Also, time since the last feeding event (set experimentally) reduced larval and nymphal fitness, whereas it increased adult female fitness. Furthermore, we found significant heritability and evolvability, that is, the potential to respond to selection, for engorgement weight and molting time across all stages but no significant heritability for feeding time. Our findings suggest that variation in tick fitness is shaped by consistent individual differences in tick quality, for which engorgement weight is a good proxy, rather than by life‐history trade‐offs.

Characterizing Heterogeneity in Neuroimaging, Cognition, Clinical Symptoms, and Genetics Among Patients With Late-Life Depression

Late-life depression (LLD) is characterized by considerable heterogeneity in clinical manifestation. Unraveling such heterogeneity might aid in elucidating etiological mechanisms and support precision and individualized medicine. To cross-sectionally and longitudinally delineate disease-related heterogeneity in LLD associated with neuroanatomy, cognitive functioning, clinical symptoms, and genetic profiles. The Imaging-Based Coordinate System for Aging and Neurodegenerative Diseases (iSTAGING) study is an international multicenter consortium investigating brain aging in pooled and harmonized data from 13 studies with more than 35 000 participants, including a subset of individuals with major depressive disorder. Multimodal data from a multicenter sample (N = 996), including neuroimaging, neurocognitive assessments, and genetics, were analyzed in this study. A semisupervised clustering method (heterogeneity through discriminative analysis) was applied to regional gray matter (GM) brain volumes to derive dimensional representations. Data were collected from July 2017 to July 2020 and analyzed from July 2020 to December 2021. Two dimensions were identified to delineate LLD-associated heterogeneity in voxelwise GM maps, white matter (WM) fractional anisotropy, neurocognitive functioning, clinical phenotype, and genetics. A total of 501 participants with LLD (mean [SD] age, 67.39 [5.56] years; 332 women) and 495 healthy control individuals (mean [SD] age, 66.53 [5.16] years; 333 women) were included. Patients in dimension 1 demonstrated relatively preserved brain anatomy without WM disruptions relative to healthy control individuals. In contrast, patients in dimension 2 showed widespread brain atrophy and WM integrity disruptions, along with cognitive impairment and higher depression severity. Moreover, 1 de novo independent genetic variant (rs13120336; chromosome: 4, 186387714; minor allele, G) was significantly associated with dimension 1 (odds ratio, 2.35; SE, 0.15; P = 3.14 ×108) but not with dimension 2. The 2 dimensions demonstrated significant single-nucleotide variant-based heritability of 18% to 27% within the general population (N = 12 518 in UK Biobank). In a subset of individuals having longitudinal measurements, those in dimension 2 experienced a more rapid longitudinal change in GM and brain age (Cohen f2 = 0.03; P = .02) and were more likely to progress to Alzheimer disease (Cohen f2 = 0.03; P = .03) compared with those in dimension 1 (N = 1431 participants and 7224 scans from the Alzheimer's Disease Neuroimaging Initiative [ADNI], Baltimore Longitudinal Study of Aging [BLSA], and Biomarkers for Older Controls at Risk for Dementia [BIOCARD] data sets). This study characterized heterogeneity in LLD into 2 dimensions with distinct neuroanatomical, cognitive, clinical, and genetic profiles. This dimensional approach provides a potential mechanism for investigating the heterogeneity of LLD and the relevance of the latent dimensions to possible disease mechanisms, clinical outcomes, and responses to interventions.

Composition of the ileum microbiota is a mediator between the host genome and phosphorus utilization and other efficiency traits in Japanese quail (Coturnix japonica)

BackgroundPhosphorus is an essential nutrient in all living organisms and, currently, it is the focus of much attention due to its global scarcity, the environmental impact of phosphorus from excreta, and its low digestibility due to its storage in the form of phytates in plants. In poultry, phosphorus utilization is influenced by composition of the ileum microbiota and host genetics. In our study, we analyzed the impact of host genetics on composition of the ileum microbiota and the relationship of the relative abundance of ileal bacterial genera with phosphorus utilization and related quantitative traits in Japanese quail. An F2 cross of 758 quails was genotyped with 4k genome-wide single nucleotide polymorphisms (SNPs) and composition of the ileum microbiota was characterized using target amplicon sequencing. Heritabilities of the relative abundance of bacterial genera were estimated and quantitative trait locus (QTL) linkage mapping for the host was conducted for the heritable genera. Phenotypic and genetic correlations and recursive relationships between bacterial genera and quantitative traits were estimated using structural equation models. A genomic best linear unbiased prediction (GBLUP) and microbial (M)BLUP hologenomic selection approach was applied to assess the feasibility of breeding for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.ResultsAmong the 59 bacterial genera examined, 24 showed a significant heritability (nominal p ≤ 0.05), ranging from 0.04 to 0.17. For these genera, six genome-wide significant QTL were mapped. Significant recursive effects were found, which support the indirect host genetic effects on the host’s quantitative traits via microbiota composition in the ileum of quail. Cross-validated microbial and genomic prediction accuracies confirmed the strong impact of microbial composition and host genetics on the host’s quantitative traits, as the GBLUP accuracies based on the heritable microbiota-mediated components of the traits were similar to the accuracies of conventional GBLUP based on genome-wide SNPs.ConclusionsOur results revealed a significant effect of host genetics on composition of the ileal microbiota and confirmed that host genetics and composition of the ileum microbiota have an impact on the host’s quantitative traits. This offers the possibility to breed for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.

Do leaf nitrogen resorption dynamics align with the slow‐fast continuum? A test at the intraspecific level

Abstract The links between internal nitrogen recycling through the process of resorption from senescing leaves, whole‐plant resource‐use strategies and performance remain elusive. Indeed, tests of such potential linkages are hampered by the classical evaluation of plant nitrogen resorption efficiency (REN) based on ‘snapshots’ of leaf nitrogen concentration from adult and senescent leaves. We significantly increased the resolution for measuring leaf nitrogen resorption by non‐destructively tracking time courses of nitrogen concentration in leaves of 137 natural Arabidopsis thaliana genotypes native to a wide range of climates across Europe, grown in a greenhouse. In addition to the classical measurement of resorption efficiency, we computed the relative maximum resorption rate of nitrogen (RRN), that is, the amount of nitrogen remobilized by a leaf per unit time and per unit nitrogen, together with slow–fast syndrome traits at the leaf and whole‐plant levels. Across genotypes, high rates and efficiencies of nitrogen resorption were associated with low specific leaf area and late flowering. The RRN showed significant heritability, genetic associations and was negatively correlated with the mean annual temperature of the native populations. By contrast, despite the evidence of a correlation with temperature, REN showed lower heritability and no evidence of genetic association, questioning the mechanisms of nitrogen resorption. Overall, our results suggest a much stronger adaptive role for leaf nitrogen resorption than previously uncovered. Read the free Plain Language Summary for this article on the Journal blog.

Genomic Predictions of Phenotypes and Pseudo-Phenotypes for Viral Nervous Necrosis Resistance, Cortisol Concentration, Antibody Titer and Body Weight in European Sea Bass.

Simple SummarySelective breeding programs based on genomic data are still not a common practice in aquaculture, although genomic selection has been widely demonstrated to be advantageous when trait phenotyping is a difficult task. In this study, we investigated the accuracy of predicting the phenotype and the estimated breeding value (EBV) of three Bayesian models and a Random Forest algorithm exploiting the information of a genome-wide SNP panel for European sea bass. The genomic predictions were developed for mortality caused by viral nervous necrosis, post-stress cortisol concentration, antibody titer against nervous necrosis virus and body weight. Selective breeding based on genomic data is a possible option for improving these traits while overcoming difficulties related to individual phenotyping of the investigated traits. Our results evidenced that the EBV used as a pseudo-phenotype enhances the predictive performances of genomic models, and that EBV can be predicted with satisfactory accuracy. The genomic prediction of the EBV for mortality might also be used to classify the phenotype for the same trait.In European sea bass (Dicentrarchus labrax L.), the viral nervous necrosis mortality (MORT), post-stress cortisol concentration (HC), antibody titer (AT) against nervous necrosis virus and body weight (BW) show significant heritability, which makes selective breeding a possible option for their improvement. An experimental population (N = 650) generated by a commercial broodstock was phenotyped for the aforementioned traits and genotyped with a genome-wide SNP panel (16,075 markers). We compared the predictive accuracies of three Bayesian models (Bayes B, Bayes C and Bayesian Ridge Regression) and a machine-learning method (Random Forest). The prediction accuracy of the EBV for MORT was approximately 0.90, whereas the prediction accuracies of the EBV and the phenotype were 0.86 and 0.21 for HC, 0.79 and 0.26 for AT and 0.71 and 0.38 for BW. The genomic prediction of the EBV for MORT used to classify the phenotype for the same trait showed moderate classification performance. Genome-wide association studies confirmed the polygenic nature of MORT and demonstrated a complex genetic structure for HC and AT. Genomic predictions of the EBV for MORT could potentially be used to classify the phenotype of the same trait, though further investigations on a larger experimental population are needed.

Heritability of social behavioral phenotypes and preliminary associations with autism spectrum disorder risk genes in rhesus macaques: A whole exome sequencing study.

Nonhuman primates and especially rhesus macaques (Macaca mulatta) have been indispensable animal models for studies of various aspects of neurobiology, developmental psychology, and other aspects of neuroscience. While remarkable progress has been made in our understanding of influences on atypical human social behavior, such as that observed in autism spectrum disorders (ASD), many significant questions remain. Improved understanding of the relationships among variation in specific genes and variation in expressed social behavior in a nonhuman primate would benefit efforts to investigate risk factors, developmental mechanisms, and potential therapies for behavioral disorders including ASD. To study genetic influences on key aspects of social behavior and interactions-individual competence and/or motivation for specific aspects of social behavior-we quantified individual variation in social interactions among juvenile rhesus macaques using both a standard macaque ethogram and a macaque-relevant modification of the human Social Responsiveness Scale. Our analyses demonstrate that various aspects of juvenile social behavior exhibit significant genetic heritability, with estimated quantitative genetic effects similar to that described for ASD in human children. We also performed exome sequencing and analyzed variants in 143 genes previously suggested to influence risk for human ASD. We find preliminary evidence for genetic association between specific variants and both individual behaviors and multi-behavioral factor scores. To our knowledge, this is the first demonstration that spontaneous social behaviors performed by free-ranging juvenile rhesus macaques display significant genetic heritability and then to use exome sequencing data to examine potential macaque genetic associations in genes associated with human ASD.