Quantitative Genetic Analysis Research Articles

Progeny Selection and Genetic Diversity in a Pinus taeda Clonal Seed Orchard

The present article describes the development of an improved Pinus taeda clonal seed orchard adapted to the edaphoclimatic conditions of Uruguay. Initially, 2068 hectares distributed in nine companies were prospected, and 124 plus trees were identified based on growth, straightness, and health traits. These trees were clonally propagated via grafting to establish a clonal seed orchard. For the genetic evaluation of the orchard, two progeny tests were carried out in the Rivera and Paysandú municipalities. Quantitative genetic analyses allowed us to identify a simple genotype–environment interaction and an expected genetic gain for volumes of 17%, 13%, and 8% for selection intensities of 12%, 25%, and 50%, respectively. Moreover, the genetic diversity of the 124 clones of the orchard was assessed using 10 microsatellite markers. The fingerprinting profiles allowed us to identify a total of 224 alleles. The polymorphism information content of the different markers was in the range of 0.594 to 0.895. The combined probability of identity and probability of identity among siblings had a discrimination power of 8.26 × 10–14 and 5.91 × 10–5, respectively. Analysis of the genetic structure demonstrated that the seed orchard population was not structured by the supplier.

88 The impact of trait measurement error on quantitative genetic analysis

Abstract The accuracy of trait measurements greatly affects the quality of downstream genetic analyses. With the advancement of three-dimensional sensor cameras and computer vision techniques, there is a growing trend to adopt these new tools for on-farm data collection as they can reduce labor and facilitate the collection of large phenotypic data sets across diverse populations. Pig body weight (BW) values estimated 1) manually using a digital scale, and 2) from videos using computer vision can be considered as two different measurements of the same trait because the source of phenotyping error is different. In other words, BW is controlled by the same set of causal loci, but by different phenotyping errors, and thus has different heritabilities. Previous research has shown that trait measurement error, defined as the difference between manually collected phenotypes and image-derived phenotypes, may be influenced, at least in part, by genetic factors. This suggests that trait measurement error is systematic rather than random, and thus, more likely to lead to misleading downstream results when used in quantitative genetic analysis. Therefore, in this study, we investigated the impact of trait measurement error on the genetic analysis of pig BW. Specifically, the objectives of this study were to 1) estimate trait measurement error from manually collected and image-derived pig BW, and 2) estimate genomic heritability for trait measurement error. Ground-truth BW data were collected manually using a digital weighing system for 540 pigs at five different time points over 3 mo. In addition, image-derived BW were estimated by training models on video data captured by a depth camera. A total of four image analysis machine learning and deep learning models were used, including adaptive thresholding segmentation coupled with either ordinary least squares or random forests, and deep regression based on ResNet50 and Xception. Coefficients of determination for image-derived and ground truth BW were at least 0.95 across time points. Genomic heritability estimates for manual and image-derived BW were mostly identical across time points (ranging from 0.23 to 0.54), indicating that manually measured and image-derived phenotypes yield the same genetic results. In addition, genomic heritability estimates for measurement error were consistently negligible, indicating that trait measurement errors in pig BW do not contain systematic errors that could bias downstream genetic analysis.

Overlooked drivers of the greenhouse effect: The nutrient-methane nexus mediated by submerged macrophytes

Submerged macrophytes remediation is a commonly used technique for improving water quality and restoring habitat in aquatic ecosystems. However, the drivers of success in the submerged macrophytes assembly process and their specific impacts on methane emissions are poorly understood. Thus, we conducted a mesocosm experiment to test the growth plasticity and carbon fixation of widespread submerged macrophytes (Vallisneria natans) under different nutrient conditions. A refined dynamic chamber method was utilized to concurrently collect and quantify methane emission fluxes arising from ebullition and diffusion processes. Significant correlations were found between methane flux and variations in the physiological activities of V. nantas by the fluorescence imaging system. Our results show that exceeding tolerance thresholds of ammonia in the water significantly interfered with the photosynthetic systems in submerged leaves and the radial oxygen loss in adventitious roots. The recovery process of V. natans accelerated the consumption of dissolved oxygen, leading to increase in the populations of methanogen (153.3 % increase of mcrA genes) and subsequently elevating CH4 emission fluxes (23.7 %) under high nutrient concentrations. Conversely, V. natans increased the available organic carbon under low nutrient conditions by radial oxygen loss, further increasing CH4 emission fluxes (94.7 %). Quantitative genetic and modeling analyses revealed that plant restoration processes drive ecological niche differentiation of methanogenic and methane oxidation microorganisms, affecting methane release fluxes within the restored area. The speciation process of V. natans is incapable of simultaneously meeting improved water purification and reduced methane emissions goals.

Quantitative genetic analysis indicate non-heritability of major fatty acid in the muscle of Chinese mitten crab (Eriocheir sinensis)

The Chinese mitten crab (Eriocheir sinensis) is a commercially important aquaculture species, and crab meat generally has the high percentage of long-chain polyunsaturated fatty acids (LC-PUFAs) in the total fatty acids, which contributes the unique flavor and high nutrition value for adult crab. Muscle is the largest edible tissue in crustaceans, containing a variety of fatty acids, and understanding the genetic parameters of fatty acids in the meat of E. sinensis would be useful for the aquaculture of this species. This study investigated the heritability, genetic and phenotypic correlations of major fatty acids in the muscle of E. sinensis. Progeny from 25 full-sib families were reared under a common environment until they reached market size, and 429 mature crabs were selected for analysis. The results showed that the heritabilities of most fatty acids were low ranged from 0.01 (n-3PUFA) to 0.21 (MUFA), but the high heritabilities were recorded for C20:3n3 and C20:3n6 with values of 0.99 and 0.32, respectively. Furthermore, the strongest positive genetic correlations were found between C20:5n3 and C22:6n3(0.99), n-3PUFA(0.99), and PUFA and LC- PUFAs (0.99), n-3PUFA(0.99), whereas the strongest phenotype correlation was found between C20:5n3 and n-3 PUFA (0.96); C20:3n6 showed a significant negative genetic correlation with C20:3n3(−0.86) and C18:0 (−0.98), whereas C20:3n6 showed significant negative phenotypic correlation with C20:3n3(−0.14), C20:5n3(−0.15) and C22:6n3(−0.18). In conclusion, the percentages of major fatty acids, particularly C20:5n3, C22: 5n3 and C20:4n6, in E. sinensis muscle have very low heritabilities, suggesting that these fatty acids contents/composition in the muscle are ineffective targets for the selective breeding programs of E. sinensis.

The spatiotemporal and genetic architecture of extraoral taste buds in Astyanax cavefish

Intense environmental pressures can yield both regressive and constructive traits through complex evolutionary mechanisms. Although regression is well-studied, the biological bases of constructive features are less well understood. Cave-dwelling Astyanax fish harbor prolific extraoral taste buds on their heads, which are absent in conspecific surface-dwellers. Here, we present novel ontogenetic data demonstrating extraoral taste buds appear gradually and late in life history. This appearance is similar but non-identical in different cavefish populations, where patterning has evolved to permit taste bud re-specification across the endoderm-ectoderm germ layer boundary. Quantitative genetic analyses revealed that spatially distinct taste buds on the head are primarily mediated by two different cave-dominant loci. While the precise function of this late expansion on to the head is unknown, the appearance of extraoral taste buds coincides with a dietary shift from live-foods to bat guano, suggesting an adaptive mechanism to detect nutrition in food-starved caves. This work provides fundamental insight to a constructive evolutionary feature, arising late in life history, promising a new window into unresolved features of vertebrate sensory organ development.

Evolution of "invasion syndrome" in invasive goldenrod is not constrained by genetic trade-offs.

A suite of plant traits is thought to make weed populations highly invasive, including vigorous growth and reproduction, superior competitive ability, and high dispersal ability. Using a breeding design and a common garden experiment, we tested whether such an "invasion syndrome" has evolved in an invasive range of Solidago altissima, and whether the evolution is likely to be genetically constrained. We found an overall shift in invasive phenotypes between native North American and invasive Japanese populations. The invasive populations were taller and produced more leaves, suggesting a superior ability to exploit limited resources. The populations also produced more allelopathic compounds that can suppress competitor growth. Finally, invasive populations produced more seeds, which are smaller and are released from a greater height, indicating a potential for superior dispersal ability than the native populations. Quantitative genetics analyses found a large amount of additive genetic variation in most focal traits across native and invasive populations, with no systematic differences in its magnitude between the ranges. Genetic covariances among three traits representing invasion strategies (leaf mass, polyacetylene concentration and seed size) were small. The R metric, which measures the effect of genetic covariances on the rate of adaptation, indicated that the covariance neither constrains nor accelerates concerted evolution of these traits. The results suggest that the invasion syndrome in S. altissima has evolved in the novel range due to ample additive genetic variation, and relatively free from genetic trade-offs.

Whole-genome resequencing identifies candidate genes and allelic variation in the MdNADP-ME promoter that regulate fruit malate and fructose contents in apple

Soluble sugar and organic acids are key determinants of fruit organoleptic quality and directly affect the commodity value and economic returns of fruit crops. We performed whole-genome sequencing of the apple varieties Gala and Xiahongrou, along with their F1 hybrids, to construct a high-density bin map. Our quantitative genetic analysis pinpointed 53 quantitative trait loci (QTLs) related to 11 sugar and acid traits. We identified a candidate gene, MdNADP-ME, responsible for malate degradation, in a stable QTL on linkage group 15. Sequence analysis revealed an A/C SNP in the promoter region (MEp-799) that influences binding of the MdMYB2 transcription factor, thereby affecting MdNADP-ME expression. In our study of various apple genotypes, this SNP has been demonstrated to be linked to malate and fructose levels. We also developed a dCAPS marker associated with fruit fructose content. These results substantiate the role of MdNADP-ME in maintaining the equilibrium between sugar and acid contents in apple fruits.

Comprehensive Clinical and Genetic Analyses of Circulating Bile Acids and Their Associations With Diabetes and Its Indices.

Bile acids (BAs) are cholesterol-derived compounds that regulate glucose, lipid, and energy metabolism. Despite their significance in glucose homeostasis, the association between specific BA molecular species and their synthetic pathways with diabetes mellitus (DM) is unclear. Here, we used a recently validated stable-isotope dilution highperformance liquid chromatography with tandem mass spectrometry (LC-MS/MS) method to quantify a panel of BAs in fasting plasma from subjects (n=2,145) and explored structural and genetic determinants of BAs linked to DM, insulin resistance and obesity. Multiple 12α-hydroxylated BAs were associated with DM [adjusted odds ratios (aORs):1.3-1.9 (all P<0.05)] and insulin resistance [aORs:1.3-2.2 (all P<0.05)]. Conversely, multiple 6a-hydroxylated BAs and isolithocholic acid (Iso-LCA) were inversely associated with DM and obesity [aORs:0.3-0.9 (all P<0.05)]. Genome-wide association studies (GWAS) revealed multiple genome-wide significant loci linked with nine of the 14 DM-associated BAs, including a locus for Iso-LCA (rs11866815). Mendelian randomization analyses showed genetically elevated DCA levels were causally associated with higher BMI, and Iso-LCA levels were causally associated with reduced BMI and DM risk. In conclusion, comprehensive large-scale quantitative mass spectrometry and genetics analyses show circulating levels of multiple structurally specific BAs, especially DCA and Iso-LCA, are clinically associated with and genetically linked to obesity and DM.

Quantitative genetic analysis of attractiveness of yeast products to Drosophila.

An attractive perfume is a complex mixture of compounds, some of which may be unpleasant on their own. This is also true for the volatile combinations from yeast fermentation products in vineyards and orchards when assessed by Drosophila. Here, we used crosses between a yeast strain with an attractive fermentation profile and another strain with a repulsive one and tested fly responses using a T-maze. QTL analysis reveals allelic variation in four yeast genes, namely PTC6, SAT4, YFL040W, and ARI1, that modulated expression levels of volatile compounds [assessed by gas chromatography-mass spectrometry (GC-MS)] and in different combinations, generated various levels of attractiveness. The parent strain that is more attractive to Drosophila has repulsive alleles at two of the loci, while the least attractive parent has attractive alleles. Behavioral assays using artificial mixtures mimicking the composition of odors from fermentation validated the results of GC-MS and QTL mapping, thereby directly connecting genetic variation in yeast to attractiveness in flies. This study can be used as a basis for dissecting the combination of olfactory receptors that mediate the attractiveness/repulsion of flies to yeast volatiles and may also serve as a model for testing the attractiveness of pest species such as Drosophila suzukii to their host fruit.

Investigation of porcine circovirus type 2 and porcine circovirus type 3 infections based on dual TaqMan fluorescent quantitative PCR method and genetic evolutionary analysis of these two viruses.

Porcine circovirus type 2 (PCV2) is the pathogen of Porcine Circovirus Associated Diseases. Porcine circovirus type 3 (PCV3) is a novel porcine circovirus associated with porcine dermatitis and nephropathy syndrome (PDNS) and reproductive failure. PCV2 is clearly pathogenic, while the pathogenicity of PCV3 remains controversial, so it is crucial to monitor the prevalence of PCV2 and PCV3 in healthy and diseased pigs to investigate the effects of PCV3 and PCV2 on the health status of pigs. Here, we developed a PCV2 and PCV3 dual TaqMan quantitative PCR (qPCR) method to test samples from healthy and diseased pigs, to clarify the differences in the positive rates and viral copy numbers of PCV2 and PCV3, and to analyze the genetic evolution and molecular characterization of the viral genomes obtained with sequence alignment and phylogenetic analysis, homology and structural analysis of Cap proteins, and selection pressure analysis. We successfully established a dual TaqMan qPCR method for PCV2 and PCV3 with good repeatability, specificity and sensitivity. In total, 1,385 samples from 15 Chinese provinces were tested with the established qPCR. The total positive rates were 37.47% for PCV3 and 57.95% for PCV2, and the coinfection rate for was 25.49%. The positive rates of PCV3 and PCV2 in 372 healthy pigs were 15.05 and 69.89%, respectively, and the coinfection rate was 12.90%. The positive rates of PCV3 and PCV2 in 246 diseased pigs were 55.69 and 83.33%, respectively, and the coinfection rate was 47.97%. Eighteen PCV3 genomes and 64 PCV2 genomes were identified, including nine each of the PCV3a-1 and PCV3b genotypes, eight of PCV2a, 16 of PCV2b, and 40 of PCV2d. The amino acid identity within the PCV3 Cap proteins was 94.00-100.0%, whereas the PCV2 Cap proteins showed an identity of 81.30-100.0%. PCV3 Cap was most variable at amino acid sites 24, 27, 77, 104 and 150, whereas PCV2 Cap had 10-13 unique sites of variation between genotypes. These results clarify the prevalence and variations of PCV2 and PCV3 in healthy and diseased pigs, which will provide a basis for the prevention and control of the two viral infections.

Genetic and phenotypic evidence of the predictive validity of preschool parent reports of hyperactivity/impulsivity and inattention.

To determine the validity of parent reports (PRs) of ADHD in preschoolers, we assessed hyperactivity/impulsivity (HI) and inattention (IN) in 1114 twins with PRs at 1.5, 2.5, 4, 5, 14, 15, and 17 years, and teacher-reports at 6, 7, 9, 10, and 12. We examined if preschool PRs (1) predict high HI/IN trajectories, and (2) capture genetic contributions to HI/IN into adolescence. Group-based trajectory analyses identified three 6-17 years trajectories for both HI and IN, including small groups with high HI (N = 88, 10.4%, 77% boys) and IN (N = 158, 17.3%, 75% boys). Controlling for sex, each unit of HI PRs starting at 1.5 years and at 4 years for IN, increased more than 2-fold the risk of belonging to the high trajectory, with incremental contributions (Odds Ratios = 2.5-4.5) at subsequent ages. Quantitative genetic analyses showed that genetic contributions underlying preschool PRs accounted for up to a quarter and a third of the heritability of later HI and IN, respectively. Genes underlying 1.5-year HI and 4-year IN contributed to 6 of 8 later HI and IN time-points and largely explained the corresponding phenotypic correlations. Results provide phenotypic and genetic evidence that preschool parent reports of HI and IN are valid means to predict developmental risk of ADHD.

Glucocorticoid-Induced Myopathy: Typology, Pathogenesis, Diagnosis, and Treatment.

Glucocorticoid-induced myopathy is a non-inflammatory toxic myopathy typified by proximal muscle weakness, muscle atrophy, fatigue, and easy fatigability. These vague symptoms coupled with underlying disorders may mask the signs of glucocorticoid-induced myopathy, leading to an underestimation of the disease's impact. This review briefly summarizes the classification, pathogenesis, and treatment options for glucocorticoid-induced muscle wasting. Additionally, we discuss current diagnostic measures in clinical research and routine care used for diagnosing and monitoring glucocorticoid-induced myopathy, which includes gait speed tests, muscle strength tests, hematologic tests, bioelectrical impedance analysis (BIA), dual-energy X-ray absorptiometry (DXA), computed tomography (CT), magnetic resonance imaging (MRI), electromyography, quantitative muscle ultrasound, histological examination, and genetic analysis. Continuous monitoring of patients receiving glucocorticoid therapy plays an important role in enabling early detection of glucocorticoid-induced myopathy, allowing physicians to modify treatment plans before significant clinical weakness arises.

Genetic correlations between liver fat content, metabolic health, and adiposity distribution in the Fels Longitudinal Study

Background and aimsHepatic steatosis is known to be heritable, but its genetic basis is mostly uncharacterized. Steatosis is associated with metabolic and adiposity features; recent studies hypothesize that shared genetic effects between these traits could account for some of the unexplained heritability. This study aimed to quantify these genetic associations in a family-based sample of non-Hispanic white adults. Methods and results704 participants (18–95 years, 55.8% female) from the Fels Longitudinal Study with an MRI assessment of liver fat were included. Quantitative genetic analyses estimated the age- and sex-adjusted heritability of individual traits and the genetic correlations within trait pairs. Mean liver fat was 5.95% (SE = 0.23) and steatosis (liver fat >5.56%) was present in 29.8% of participants. Heritability (h2± SE) of steatosis was 0.72 ± 0.17 (p = 6.80e−6). All other traits including liver enzymes, fasting glucose, HOMA-IR, visceral and subcutaneous adipose tissue (VAT, SAT), body mass index, body fat percent, waist circumference, lipids and blood pressure were also heritable. Significant genetic correlations were found between liver fat and all traits except aspartate aminotransferase (AST), and among most trait pairs. Highest genetic correlations were between liver fat and HOMA-IR (0.85 ± 0.08, p = 1.73e−8), fasting glucose and ALT (0.89 ± 0.26, p = 6.68e−5), and HOMA-IR with: waist circumference (0.81 ± 0.12, p = 3.76e−6), body fat percent (0.78 ± 0.12 p = 2.42e−5) and VAT (0.73 ± 0.07, p = 6.37e−8). ConclusionsCommon genes may exist between liver fat accumulation, metabolic features and adiposity phenotypes.

Systems genetics analysis reveals the common genetic basis for pain sensitivity and cognitive function.

There is growing evidence of a strong correlation between pain sensitivity and cognitive function under both physiological and pathological conditions. However, the detailed mechanisms remain largely unknown. In the current study, we sought to explore candidate genes and common molecular mechanisms underlying pain sensitivity and cognitive function with a transcriptome-wide association study using recombinant inbred mice from the BXD family. The pain sensitivity determined by Hargreaves' paw withdrawal test and cognition-related phenotypes were systematically analyzed in 60 strains of BXD mice and correlated with hippocampus transcriptomes, followed by quantitative trait locus (QTL) mapping and systems genetics analysis. The pain sensitivity showed significant variability across the BXD strains and co-varies with cognitive traits. Pain sensitivity correlated hippocampual genes showed a significant involvement in cognition-related pathways, including glutamatergic synapse, and PI3K-Akt signaling pathway. Moreover, QTL mapping identified a genomic region on chromosome 4, potentially regulating the variation of pain sensitivity. Integrative analysis of expression QTL mapping, correlation analysis, and Bayesian network modeling identified Ring finger protein 20 (Rnf20) as the best candidate. Further pathway analysis indicated that Rnf20 may regulate the expression of pain sensitivity and cognitive function through the PI3K-Akt signaling pathway, particularly through interactions with genes Ppp2r2b, Ppp2r5c, Col9a3, Met, Rps6, Tnc, and Kras. Our study demonstrated that pain sensitivity is associated with genetic background and Rnf20-mediated PI3K-Akt signaling may involve in the regulation of pain sensitivity and cognitive functions.

Genetic basis and repeatability for desiccation resistance in Drosophila melanogaster (Diptera: Drosophilidae).

Dehydration is a stress factor for organisms inhabiting natural habitats where water is scarce. Thus, it may be expected that species facing arid environments will develop mechanisms that maximize resistance to desiccation. Insects are excellent models for studying the effects of dehydration as well as the mechanisms and processes that prevent water loss since the effect of desiccation is greater due to the higher area/volume ratio than larger animals. Even though physiological and behavioral mechanisms to cope with desiccation are being understood, the genetic basis underlying the mechanisms related to variation in desiccation resistance and the context-dependent effect remain unsolved. Here we analyze the genetic bases of desiccation resistance in Drosophila melanogaster and identify candidate genes that underlie trait variation. Our quantitative genetic analysis of desiccation resistance revealed sexual dimorphism and extensive genetic variation. The phenotype-genotype association analyses (GWAS) identified 71 candidate genes responsible for total phenotypic variation in desiccation resistance. Half of these candidate genes were sex-specific suggesting that the genetic architecture underlying this adaptive trait differs between males and females. Moreover, the public availability of desiccation data analyzed on the same lines but in a different lab allows us to investigate the reliability and repeatability of results obtained in independent screens. Our survey indicates a pervasive micro-environment lab-dependent effect since we did not detect overlap in the sets of genes affecting desiccation resistance identified between labs.

A medium-density genotyping platform for cultivated strawberry using DArTag technology.

Genomic prediction in breeding populations containing hundreds to thousands of parents and seedlings is prohibitively expensive with current high-density genetic marker platforms designed for strawberry. We developed mid-density panels of molecular inversion probes (MIPs) to be deployed with the "DArTag" marker platform to provide a low-cost, high-throughput genotyping solution for strawberry genomic prediction. In total, 7742 target single nucleotide polymorphism (SNP) regions were used to generate MIP assays that were tested with a screening panel of 376 octoploid Fragaria accessions. We evaluated the performance of DArTag assays based on genotype segregation, amplicon coverage, and their ability to produce subgenome-specific amplicon alignments to the FaRR1 assembly and subsequent alignment-based variant calls with strong concordance to DArT's alignment-free, count-based genotype reports. We used a combination of marker performance metrics and physical distribution in the FaRR1 assembly to select 3K and 5K production panels for genotyping of large strawberry populations. We show that the 3K and 5K DArTag panels are able to target and amplify homologous alleles within subgenomic sequences with low-amplification bias between reference and alternate alleles, supporting accurate genotype calling while producing marker genotypes that can be treated as functionally diploid for quantitative genetic analysis. The 3K and 5K target SNPs show high levels of polymorphism in diverse F. × ananassa germplasm and UC Davis cultivars, with mean pairwise diversity (π) estimates of 0.40 and 0.32 and mean heterozygous genotype frequencies of 0.35 and 0.33,respectively.

The first two chromosome-scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus.

The native, perennial shrub American hazelnut (Corylus americana) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high-value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high-quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome-scale assemblies for this species using the accessions 'Rush' and 'Winkler'. Genomes were assembled using HiFi PacBio reads and Arima Hi-C data, and Oxford Nanopore reads and a high-density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for 'Rush' and 'Winkler', respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. 'Rush' has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while 'Winkler' had corresponding scores of 96.9 and 96.5, indicating high-quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana, as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high-density SNP marker sets from genotyping-by-sequencing data using 1343 C. americana, C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self-incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self-incompatibility in Corylus.

Evaluating alternative models of youth externalizing using quantitative genetic analyses.

Interest has increased in the recent literature on characterizing psychopathology dimensionally in hierarchical models. One dimension of psychopathology that has received considerable attention is externalizing. Although extensively studied and well-characterized in late adolescents and adults, delineation of the externalizing spectrum in youth has lagged behind. As a complement to structural analyses of externalizing, in this study, we use quantitative genetic analyses of twin data to adjudicate among alternative models of youth externalizing that differ in granularity. Specifically, we compared model fit, estimates of genetic and environmental influences on the externalizing dimension, and the average, variability, and precision of genetic and environmental influences on individual symptoms due to the externalizing dimension, specific symptom dimensions, and unique etiological influences. Given that none of these criteria are definitive on their own, we looked to the confluence of these criteria to exclude particular models while highlighting others as leading contenders. We analyzed parent-report data on 38 externalizing symptoms from a population-representative, ethnically diverse sample of 883 youth twin pairs (51% female), who were on average 8.5 years old. Although models including an externalizing composite and attention deficit hyperactivity disorder, oppositional defiant disorder, and conduct disorder diagnoses and symptom dimensions showed similar heritability to latent variable models of externalizing, models that included latent dimensions of externalizing and more fine-grained symptom dimensions fit better and were more balanced in the magnitude of genetic and environmental influences on individual symptoms due to the externalizing dimension and specific symptom dimensions. Pending replication, these more granular and elaborated model(s) can be useful for advancing research on causes and outcomes of youth externalizing and its fine-grained specific components. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Pleiotropic fitness effects across sexes and ages in the Drosophila genome and transcriptome.

Selection varies between categories of individuals, with far-reaching ramifications: Sex-specific selection can impede or accelerate adaptation, and differences in selection between young and old individuals are ultimately responsible for senescence. Here, we measure early- and late-life fitness in adults of both sexes from the Drosophila genetic reference panel and perform quantitative genetic and transcriptomic analyses. Fitness was heritable, showed positive pleiotropy across sexes and age classes, and appeared to be influenced by very large numbers of loci with small effects plus a smaller number with moderate effects. Most loci affected male and female fitness in the same direction; relatively few candidate sexually antagonistic loci were found, though these were enriched on the X chromosome as predicted by theory. The expression level of many genes showed an opposite correlation with fitness in males and females, consistent with unresolved sexual conflict over transcription. The load of deleterious mutations correlated negatively with fitness across genotypes, and we found some evidence for the mutation accumulation (but not the antagonistic pleiotropy) theory of aging.

Identification of sex-linked SNP markers in wild populations of monomorphic birds.

Single-nucleotide polymorphism (SNP) analysis is a powerful tool for population genetics, pedigree reconstruction and phenotypic trait mapping. However, the untapped potential of SNP markers to discriminate the sex of individuals in species with reduced sexual dimorphism or of individuals during immature stages remains a largely unexplored avenue. Here, we developed a novel protocol for molecular sexing of birds based on the detection of unique Z- and W-linked SNP markers. Our method is based on the identification of two unique loci, one in each sexual chromosome. Individuals are considered males when they show no calls for the W-linked SNP and are heterozygous or homozygous for the Z-linked SNP, while females exhibit both Z- and W-linked SNP calls. We validated the method in the Jackdaw (Corvus monedula). The reduced sexual dimorphism in this species makes it difficult to identify the sex of individuals in the wild. We assessed the reliability of the method using 36 individuals of known sex and found that their sex was correctly assigned in 100% of cases. The sex-linked markers also proved to be widely applicable for discriminating males and females from a sample of 927 genotyped individuals at different maturity stages, with an accuracy of 99.5%. Since SNP markers are increasingly used in quantitative genetic analyses of wild populations, the approach we propose has great potential to be integrated into broader genetic research programmes without the need for additional sexing techniques.