Phenotypic Variation Research Articles

Conversion of social organization in fire ants induced by few colony members: Unmasking indirect genetic effects

Genes and the environment jointly shape individual traits, but the influence of indirect genetic effects (IGEs), arising from the genetic composition of interacting conspecific individuals, is often ignored or underemphasized. Moreover, because of practical challenges in characterizing IGEs, empirical research has fallen behind theoretical advancement. The fire ant Solenopsis invicta offers a uniquely suitable study system due to its distinct colony-level phenotypic variation (monogyne and polygyne social forms) attributed to IGEs of a social-supergene variant (b allele). A minority of b-carrying workers (Bb genotype) can trigger colony-level conversion from monogyne (single queen per colony) to polygyne (multiple queens per colony) behavior. This study investigated the mechanisms underlying this process via 400-ant microcolonies. We first showed that assimilated Bb workers reduce aggression by host BB workers toward Bb queens, thus inducing polygyny, at rates observed earlier in experiments that used full-size (>20,000 ants) colonies. We then demonstrated that social conversion is facilitated by cuticular contact between the worker types, and verified the presence of nonvolatile cuticular pheromones that are necessary but not sufficient components underpinning this process. Follow-up experiments suggested that a second, polygyne worker-produced pheromone that is only released once such workers detect a Bb queen is also necessary but again insufficient, for full expression of the conversion phenomenon. Thus, multiple pheromonal components linked to presence of the b supergene allele in colony workers appear to be involved in shaping social environments and thereby inducing, via IGEs, the transformation from monogyne to polygyne fire ant societies.

Assessment of phenotypic variability in garden cress (Lepidium sativum L.) using morphological traits across contrasting environments

Assessment of phenotypic variability in garden cress (Lepidium sativum L.) using morphological traits across contrasting environments

Systems genetics reveals the influence of eQTLs in mouse embryonic stem cells on transcriptional variation later in differentiated neural progenitor cells.

Genetic variation leads to phenotypic variability in pluripotent stem cells that presents challenges for regenerative medicine. Although recent studies have investigated the impact of genetic variation on pluripotency maintenance and differentiation capacity, less is known about how genetic variants affecting the pluripotent state influence gene regulation later in development. Here, we characterized expression of 12,000 genes in a large panel of donor-matched Diversity Outbred (DO) mouse embryonic stem cell (mESC) and neural progenitor cell (mNPC) lines. Quantitative trait locus (QTL) mapping identified 4,060 expression QTL (eQTL) in mNPCs, including 2,998 local and 1,062 distant eQTL. In a comparison of mNPC and mESC eQTLs, we found that local eQTLs were more likely than distant eQTL to be detected in both cell types. Distant eQTL were largely unique to one cell type, and we mapped three mNPC-specific eQTL hotspots on Chromosomes (Chrs) 1, 10, and 11. Mediation analysis of the Chr 1 hotspot identified Rnf152 as the best candidate mediator expressed in mNPCs, while cross-cell type mediation using mESC gene expression along with partial correlation analysis strongly implicated genetic variant(s) affecting Pign expression in the mESC state as regulating the mNPC Chr 1 hotspot. These findings highlight that local mNPC eQTL are more likely than distant eQTL to be shared with mESCs; distant mNPC eQTL are numerous but largely unique to that cell type, with many co-localizing to mNPC-specific hotspots; and mediation analysis across cell types suggests that expression of Pign in mESCs shapes the transcriptome of the more specialized mNPC state.

Experimental Evolution of Phytophthora infestans on Tomato Reveals Rapid Genotypic and Phenotypic Adaptation and Dynamic RXLR Genome Variation.

The late blight pathogen, Phytophthora infestans, poses a significant threat to tomato crops worldwide. To understand the potential for rapid adaptation of this pathogen, we conducted an "in vitro" experimental evolution study with four P. infestans US-23 lineages collected from tomato hosts with different combinations of resistance genes (Ph genes). These isolates were passed serially over 8 generations on five tomato cultivars. After infection, targeted sequencing of the pathogen's RXLR effector genes was done. In just eight generations, we observed both phenotypic and genotypic changes in the US-23 lineages, with differences in disease severity among pathogen isolates and alterations in the RXLR genome. Our findings suggest rapid mutation even in a clonally reproducing lineage, highlighting the potential for adaptation of P. infestans within a single growing season on tomato. These insights shed light on the adaptability of this devastating pathogen and emphasize the importance of considering tomato host resistance in late blight management strategies.

Enhancing the breeding gene pool of wheat using accessions in gene banks as demonstrated by the Watkins collection.

This study demonstrates an approach to identify accessions carrying desirable alleles affecting traits of breeding interest, paving the way for the development of environmentally resilient cultivars. Recent advances in genome technology have opened opportunities to explore old germplasm collections for accessions possessing traits valuable in cultivar development. This study analyzed genotypic and phenotypic data from the pre-Green Revolution Watkins collection, to find loci linked to climate adaptation and rust resistance (leaf, stem, and stripe) using genome scans and single-nucleotide polymorphism (SNP)-level fixation index (FST) analysis. Key signature regions were revealed on chromosomes 2A and 3B. Consistent with the past findings, a highly differentiated region was detected on 6B in the cultivar subset of the collection, highlighting this region a breeding target. Chromosome-based scans located a region previously associated with RVA peak viscosity and breakdown, spanning 12.5Mb and 13Mb on 7D, harboring 13 genes, including the most pleiotropic TRAESCS7D02G026700 (ET2/AP2/ERF). SNP-FST analysis noticeably differentiated several loci between spring and winter wheat, including 5A:582,550,290 linked to the Vrn-A1 gene. Likewise, SNP-level FST analysis between rust resistant and susceptible accessions detected loci associated with resistance such as 1B:670,137,479-670,543,997 linked to Lr46/Yr29, and 2B:763,926,560 in a region harboring the Yr7/Yr5/YrSP gene cluster. Significant phenotypic variation was observed between the resistant and susceptible alleles at the high-FST loci indicating the role of these loci in disease resistance. At all the top ten high-FST loci, eight and thirteen accessions carried the resistance alleles for leaf and stripe rust, respectively, suggesting these accessions as potential pre-breeding candidates. This study highlights how historic germplasm collections, combined with their genetic and environmental data, can enhance breeding diversity and identify pre-breeding materials for developing resilient cultivars.

MRAS: Master Regulator Analysis of Alternative Splicing.

As a molecular feature that characterizes most tumor types, cancer-associated splicing dysregulation largely arises from recurrent genetic mutations and altered expression of trans-acting splicing factors. Although splicing factor mutations occur less frequently in solid tumors, splicing disorders are pervasive and proven to promote tumorigenesis. However, it still lacks an efficient way to identify the key splicing factors at the top regulatory hierarchy whose abnormal expressions induce such splicing disorders and drive phenotypic variability. Here, MRAS (Master Regulator analysis of Alternative Splicing) is introduced, a computational method designed to pinpoint the pivotal splicing factors that play a central role in shaping splicing regulatory networks and influencing cellular processes. MRAS is demonstrated its power by identifying master splicing regulators associated with various disease phenotypes, including tumor initiation, progression, metastasis, and treatment resistance. Moreover, by applying MRAS to single-cell RNA-seq data, crucial regulatory relationships that govern cell-type specific splicing programs have been uncovered. Overall, MRAS presented as an accurate and versatile approach to unraveling the underlying mechanism of splicing regulation.

Behavioral DiverCity: Individual differences in behavior change along an urbanization gradient

Abstract Urbanization is occurring globally at an unprecedented rate and, despite the eco-evolutionary importance of individual variation, we still have limited insight on how phenotypic variation is modified by anthropogenic environmental change. Urbanization can increase individual differences in some contexts, but whether this is generalizable to behavioral traits, which directly affect how organisms interact with, and respond to, environmental variation, is not well known. Here we examined variation across three behavioral traits linked to stress reactivity, anti-predator response, and novelty-coping (breath rate, handling aggression, and exploration behavior) in great tits Parus major along an urbanization gradient. We phenotyped > 1000 individuals across nine years, to test whether individual differences in behavior increased with urbanization and spatial environmental heterogeneity. We used two different approaches: a city vs. forest comparison (i.e., a binary descriptor) and an urbanization gradient approach (i.e., a continuous quantitative score from 0 to 1) to explore the influence of built-up areas at different spatial scales. Our results reveal that urban individuals display more diverse stress-related and anti-predator behaviors (breath rate and handling aggression), yet show more similarity in their exploratory behavior than forest counterparts. However, there was no evidence that individual variation changes along the percentage of built-up areas for any traits. This study suggest that generalizations about how behavioral traits respond to urbanization will differ across behavioral dimensions. In particular, we may expect decreased individual diversity in urban birds for traits related to behavioral response to novelty.

Colorimetric skin tone scale for improved accuracy of human skin tone annotations.

Human image datasets used to develop and evaluate technology should represent the variation in human phenotypes, including skin tone. Datasets that include skin tone information frequently rely on manual skin tone ratings based on the Fitzpatrick Skin Type (FST) or the Monk Skin Tone (MST) scales in lieu of the actual measured skin tone of the image dataset subjects. However, perceived skin tone is subject to known perceptual errors and skin tone appearance in digital images can vary substantially depending on the capture camera and environment, confounding manual ratings. Surprisingly, the relationship between skin tone ratings and measured skin tone has not been explored. To close this research gap, we measured the relationship between skin tone ratings from existing scales (FST, MST) and skin tone values measured by a calibrated colorimeter. We also propose and assess a novel Colorimetric Skin Tone (CST) scale developed based on prior colorimetric measurements. Using experiments requiring humans to rate their own skin tone and the skin tone of subjects in images, we show that the new CST scale is more sensitive, consistent, and colorimetrically accurate. While skin tone ratings appeared to correct for some color variation across images, they introduced perceptual errors related to race and other factors. These perceptual errors must be considered before using manual skin-tone ratings in technology evaluations or for engineering decisions.

Plant genotype-specific modulation of Clonostachys rosea-mediated biocontrol of septoria tritici blotch disease in wheat

BackgroundBeneficial microorganisms can act as biological control agents (BCAs) directly by targeting pathogens or indirectly by enhancing the plant’s defense mechanisms against pathogens. However, efficiencies with which plants benefit from BCAs vary, potentially because of genetic variation in plants for plant-BCA compatibility. The aim of this study was to explore the genetic variation in winter wheat for modulation of Clonostachys rosea-mediated biocontrol of septoria tritici blotch disease caused by the fungal pathogen Zymoseptoria tritici.ResultsIn total, 202 winter wheat genotypes, including landraces and old cultivars grown from 1900 onwards in the Scandinavian countries, were tested under greenhouse-controlled conditions. Foliar spray applications of the pathogen and the fungal BCA in two treatments, i.e., Z. tritici (Zt) alone and Z. tritici along with C. rosea (ZtCr) were used to assess the disease progress over time. The absence and presence of C. rosea in Zt and ZtCr, respectively, allowed the dissection of variation for plant disease resistance and biocontrol efficacy. The study showed significant (P < 0.05) phenotypic variation among plant genotypes for disease progression in both Zt and ZtCr treatments. Moreover, the application of C. rosea resulted in a significant (P < 0.05) reduction in disease progression for seven genotypes and increased disease progression for eleven genotypes, indicating a plant genotype-dependent effect on the interaction between wheat, C. rosea and Z. tritici. For the phenotypic variation in disease progress and biocontrol efficacy, a genome-wide association study using a 20K single-nucleotide polymorphism (SNP) marker array was also performed. In total, five distinct SNP markers associated with disease resistance and four SNP markers associated with C. rosea biocontrol efficacy were identified.ConclusionsThis work serves as a foundation to further characterize the genetic basis of plant-BCA interactions when inoculated with Z. tritici, facilitating opportunities for simultaneous breeding for disease resistance and biocontrol efficacy.

Dynamics of neutrophil phenotype and function in sickle cell disease

IntroductionWhile sickle cell disease (SCD) is primarily acknowledged as an erythrocyte disorder, emerging evidence suggests a role for altered neutrophil phenotype and function in SCD pathophysiology and disease severity. Given the conflicting findings in previous studies, we performed a comprehensive exploration of neutrophil characteristics in SCD patients during steady state and vaso-occlusive crisis (VOC), as well as in response to therapeutic interventions.MethodsNeutrophil phenotype was assessed by flow cytometry and functional properties were evaluated by measurement of neutrophil adhesion and reactive oxygen species (ROS) production.ResultsA total of 49 SCD patients (of whom 19 during both steady state and VOC) along with 16 healthy ethnicity-matched and 30 non-matched controls, were included in the study. Differences were observed between neutrophils from patients compared to controls and between control groups. Neutrophil phenotype was more activated in SCD patients compared to non-matched controls. Neutrophil adhesion was increased in steady-state SCD patients compared to both ethnicity-matched and non-matched controls.DiscussionWhile neutrophil phenotype in SCD patients differed from non-matched controls, in contrast to earlier studies, the differences in neutrophil phenotype between SCD patients and ethnicity-matched controls were modest. In vitro neutrophil adhesion was higher in SCD patients than in ethnicity-matched and non-matched controls. Potential explanations for the discrepancies between earlier findings and our study are the large variation in neutrophil phenotypes between individuals, methodological variability between studies and differences in the time interval between blood sample collection and the measurements.

DNA methylation patterns linked to salinity and geography in the American eel (Anguilla rostrata)

Abstract The panmictic American eel (Anguilla rostrata) displays a wide range of intraspecific phenotypic variation as well as geographical sex bias and differential recruitment. By definition, panmictic species lack genetic structure, thus local adaptation through genetic variation cannot explain the presence of intraspecific variation. As a result, the contrasting phenotypes observed in the American eel could be attributed to either spatially varying selection, phenotypic plasticity (often mediated through epigenetic changes), or the interaction of both processes. Here we explore, for the first time, the role of DNA methylation in acclimatization in a panmictic species, the American eel, as well as its association with salinity and geography in Northeastern Canada. Using whole genome bisulfite sequencing in 72 individuals, we found that DNA methylation patterns were associated with geography and to a lesser degree with salinity. We identified a genomic region with differential methylation associated with salinity that falls inside the SOCS2 gene, which has been previously linked to salinity differences in other fish species, as well as to metabolism and somatic growth regulation. This study advances our understanding of how panmictic species or populations with high gene flow acclimatize to variable environments in the absence of heritable genetic local adaptation.

Research on the Reproductive Strategies of Different Provenances/Families of Juglans mandshurica Maxim. Based on the Fruit Traits

This study systematically analyzed the fruit traits of four sources and 117 families of Juglans mandshurica Maxim. in Jilin Province. By measuring key traits such as fruit phenotype and nut phenotype, the relationship between fruit characteristics and environmental adaptability was explored, leading to the selection of superior materials with high oil content potential. The study used fruit from J. mandshurica of 117 families (random sampling) across four provenances as experimental materials and measured 13 fruit phenotypic traits, including fruit length and fruit width. Finally, principal component analysis and genetic variation parameters were conducted. The results of the variance analysis (ANOVA) indicated that except for the nut roundness index, all other traits exhibited highly significant differences among provenances and families (p &lt; 0.01). The range of genetic and phenotypic variation coefficients for the various traits was 7.47–23.23% and 8.76–29.59%. The family heritability ranged from 0.968 to 0.988. Correlation analysis among fruit traits revealed a non-significant correlation between fruit width and seed yield, fruit type index and nut weight, kernel weight and kernel yield, as well as nut longitudinal diameter and kernel yield. However, significant correlations were observed among all other traits. The Pearson correlation analysis between fruit traits and environmental factors revealed a significant negative correlation between longitude and seed yield. Cluster analysis results, based on the Euclidean distance method, showed that materials from four provenances were categorized into three groups at a genetic distance of 5. Principal Component Analysis (PCA) revealed that the cumulative contribution rate of four principal components reached 87.00%. PCI demonstrated the highest contribution rate and included traits such as fruit length, nut longitudinal diameter, nut transverse diameter, nut side diameter, three-diameter mean, and nut weight. One elite provenance and five elite families were preliminarily selected. The realized gain for the selected provenance fruit traits was higher for fruit weight and kernel weight, with values of 2.41% and 3.67%, respectively. For the selected families, the genetic gain was highest for kernel yield and kernel weight, with values of 16.51% and 26.66%, respectively. The findings will provide insights into breeding strategies to enhance walnut oil yield. The identified traits may be used to guide breeding programs for developing high-oil-content varieties; However, further validation studies are required to confirm these traits and their applicability in large-scale breeding efforts.

Molecular dissection of the genetic architecture of phenology underlying Lupinus hispanicus early flowering and adaptation to winter- or spring sowing

Spanish lupin, Lupinus hispanicus Boiss. et Reut. is an untapped grain legume species characterized by moderate frost resistance, tolerance to poor soil and waterlogging, high yield stability, and remarkable seed protein content. It has been recognized as a good candidate for domestication to broaden the palette of crop diversity. One of the key characteristics that need to be precisely addressed during domestication is the vernalization responsiveness of flowering, which is advantageous in autumn sowing due to improved frost tolerance, whilst undesired in spring sowing as it delays flowering. Ahead of L. hispanicus breeding, in the present work, we aimed to recognize existing phenotypic variability of flowering time and vernalization response and to evaluate the genetic architecture of early and late phenology by DArT-seq genotyping and genome-wide association study (GWAS) in world germplasm collection of the species. Controlled environment phenotyping revealed high variability of flowering time and vernalization responsiveness and significant correlations with population structure. DArT-seq genotyping yielded 23 728 highly polymorphic markers distributed extensively across all 26 chromosomes. GWAS identified a number of markers significantly associated with flowering time with or without pre-sowing vernalization, including those overlapping with the two major quantitative trait loci reported previously for white lupin species. Microsynteny-based analysis of the genetic content of L. hispanicus genome regions carrying significantly associated markers highlighted several candidate genes from photoperiodic and vernalization pathways. To summarize, the present study identified germplasm resources for autumn- and spring-sown cultivation of L. hispanicus and provided tools for marker-assisted selection towards required flowering phenology.

Phenotypic plasticity of Eurohypnum leptothallum in degraded karst ecosystems: Adaptative mechanisms and ecological functions driven by warming temperatures.

Phenotypic plasticity of Eurohypnum leptothallum in degraded karst ecosystems: Adaptative mechanisms and ecological functions driven by warming temperatures.

Whole-genome resequencing reveals the population structure and domestication processes of endemic endangered goose breeds (Anser cygnoides).

Whole-genome resequencing reveals the population structure and domestication processes of endemic endangered goose breeds (Anser cygnoides).

Proteomics of Sternaspis chinensis to understand phosphate biomineralization in annelids.

Proteomics of Sternaspis chinensis to understand phosphate biomineralization in annelids.

Transcripts and genomic intervals associated with variation in metabolite abundance in maize leaves under field conditions

Plants exhibit extensive environment-dependent intraspecific metabolic variation, which likely plays a role in determining variation in whole plant phenotypes. However, much of the work seeking to use natural variation to link genes and transcript’s impacts on plant metabolism has employed data from controlled environments. Here, we generated and analyzed data on the variation in the abundance of 26 metabolites across 660 maize inbred lines under field conditions. We employ these data and previously published transcript and whole plant phenotype data reported for the same field experiment to identify both genomic intervals (through genome-wide association studies (GWAS)) and transcripts (using both transcriptome-wide association studies (TWAS) and an explainable artificial intelligence (AI) approach based on random forest (RF)) associated with variation in metabolite abundance. Both genome-wide association and random forest-based methods identified substantial numbers of significant associations including genes with plausible links to the metabolites they are associated with. In contrast, the transcriptome-wide association identified only six significant associations. In three cases, genetic markers associated with metabolic variation in our study colocalized with markers linked to variation in non-metabolic traits scored in the same experiment. We speculate that the poor performance of transcriptome-wide association studies in identifying transcript-metabolite associations may reflect a high prevalence of non-linear interactions between transcripts and metabolites and/or a bias towards rare transcripts playing a large role in determining intraspecific metabolic variation.

Comparison of circulating immune signatures across different consensus molecular subtypes (CMS) and between left- and right-sided lesions in stage II colorectal cancer using single-cell mass cytometry

BackgroundPatients with stage II colorectal cancer (CRC) show considerable variability in prognosis. Circulating immune cells play a vital role in systemic tumor surveillance. This study aimed to determine the clinical significance of the frequency and phenotype of circulating immune cell subsets in patients with stage II CRC.MethodsWe applied a 37-marker-cell-lineage-agnostic panel to perform single-cell mass cytometry on peripheral blood mononuclear cells (PBMCs) from 73 patients with stage II CRC and 21 patients with stage III CRC. To categorize the stage II patients into consensus molecular subtypes (CMS), we performed RNA sequencing on tumor and adjacent normal tissues from 51 of the 73 patients. We then compared the immune cell phenotypes and frequencies based on tumor location and CMS classification in patients with stage II CRC. Wilcoxon test was employed to compare the mean frequencies of cell clusters between different tumor locations. Krustal–Wallis analysis with post-hoc Dunn test was used to assess differences across multiple CMS groups.ResultsStage II CRC patients with left- and right-sided tumors, as well as in different CMS groups, exhibit significantly different tumor characteristics. Single-cell mass cytometry revealed profound interpatient variability in immune cell subpopulation distribution and phenotypes in PBMCs in stage II CRC. We identified unique T:monocyte complexes in the peripheral blood of patients with stage II CRC, with significantly higher frequencies in these patients compared to those with stage III CRC. Left- and right-sided stage II CRCs differed in peripheral immunity. Patients with right-sided CRC had significantly higher frequencies of circulating CD8+CD27-CD28- immunosenescent T cell subsets compared to patients with left-sided CRC. Significant variations were observed in the subpopulations of the T:monocyte complex, T cells, and monocytes across different CMS groups Patients with CMS1 tumors (immune-active) exhibited significantly higher frequencies of CD4+ central memory and CD8+ terminal effector T cell: classical monocyte complexes, as well as CD8+ terminal effector T cells in the circulation.ConclusionsThe frequency and phenotype of circulating immune cells are influenced by tumor side and CMS subtypes in stage II CRC. These observations provide a basis for further investigation into the mechanisms linking tumors and systemic immunity.

Impact of variation in CYP3A and CYP2C8 on tucatinib metabolic clearance in human liver microsomes.

Impact of variation in CYP3A and CYP2C8 on tucatinib metabolic clearance in human liver microsomes.

Female autism categorization using CNN based NeuroNet57 and ant colony optimization.

Female autism categorization using CNN based NeuroNet57 and ant colony optimization.