Multiple genetic loci affect place learning and memory performance in Drosophila melanogaster

Naturally segregating genetic variants contribute to thermal tolerance in a Drosophila melanogaster model system

Thermal tolerance is a fundamental physiological complex trait for survival in many species. For example, everyday tasks such as foraging, finding a mate, and avoiding predation are highly dependent on how well an organism can tolerate extreme temperatures. Understanding the general architecture of the natural variants within the genes that control this trait is of high importance if we want to better comprehend thermal physiology. Here, we take a multipronged approach to further dissect the genetic architecture that controls thermal tolerance in natural populations using the Drosophila Synthetic Population Resource as a model system. First, we used quantitative genetics and Quantitative Trait Loci mapping to identify major effect regions within the genome that influences thermal tolerance, then integrated RNA-sequencing to identify differences in gene expression, and lastly, we used the RNAi system to (1) alter tissue-specific gene expression and (2) functionally validate our findings. This powerful integration of approaches not only allows for the identification of the genetic basis of thermal tolerance but also the physiology of thermal tolerance in a natural population, which ultimately elucidates thermal tolerance through a fitness-associated lens.

Gene expression variation underlying tissue-specific responses to copper stress in Drosophila melanogaster

Copper is one of a handful of biologically necessary heavy metals that is also a common environmental pollutant. Under normal conditions, copper ions are required for many key physiological processes. However, in excess, copper results in cell and tissue damage ranging in severity from temporary injury to permanent neurological damage. Because of its biological relevance, and because many conserved copper-responsive genes respond to nonessential heavy metal pollutants, copper resistance in Drosophila melanogaster is a useful model system with which to investigate the genetic control of the heavy metal stress response. Because heavy metal toxicity has the potential to differently impact specific tissues, we genetically characterized the control of the gene expression response to copper stress in a tissue-specific manner in this study. We assessed the copper stress response in head and gut tissue of 96 inbred strains from the Drosophila Synthetic Population Resource using a combination of differential expression analysis and expression quantitative trait locus mapping. Differential expression analysis revealed clear patterns of tissue-specific expression. Tissue and treatment specific responses to copper stress were also detected using expression quantitative trait locus mapping. Expression quantitative trait locus associated with MtnA, Mdr49, Mdr50, and Sod3 exhibited both genotype-by-tissue and genotype-by-treatment effects on gene expression under copper stress, illuminating tissue- and treatment-specific patterns of gene expression control. Together, our data build a nuanced description of the roles and interactions between allelic and expression variation in copper-responsive genes, provide valuable insight into the genomic architecture of susceptibility to metal toxicity, and highlight candidate genes for future functional characterization.

Naturally segregating genetic variants contribute to thermal tolerance in a D. melanogaster model system

Thermal tolerance is a fundamental physiological complex trait for survival in many species. For example, everyday tasks such as foraging, finding a mate, and avoiding predation, are highly dependent on how well an organism can tolerate extreme temperatures. Understanding the general architecture of the natural variants of the genes that control this trait is of high importance if we want to better comprehend how this trait evolves in natural populations. Here, we take a multipronged approach to further dissect the genetic architecture that controls thermal tolerance in natural populations using the Drosophila Synthetic Population Resource (DSPR) as a model system. First, we used quantitative genetics and Quantitative Trait Loci (QTL) mapping to identify major effect regions within the genome that influences thermal tolerance, then integrated RNA-sequencing to identify differences in gene expression, and lastly, we used the RNAi system to 1) alter tissue-specific gene expression and 2) functionally validate our findings. This powerful integration of approaches not only allows for the identification of the genetic basis of thermal tolerance but also the physiology of thermal tolerance in a natural population, which ultimately elucidates thermal tolerance through a fitness-associated lens.

Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain

BACKGROUND

Functional genomic analyses rely on high-quality genome assemblies and annotations. Highly contiguous genome assemblies have become available for a variety of species, but accurate and complete annotation of gene models, inclusive of alternative splice isoforms and transcription start and termination sites, remains difficult with traditional approaches.

RESULTS

Here, we utilized full-length isoform sequencing (Iso-Seq), a long-read RNA sequencing technology, to obtain a comprehensive annotation of the transcriptome of the ant Harpegnathos saltator. The improved genome annotations include additional splice isoforms and extended 3' untranslated regions for more than 4000 genes. Reanalysis of RNA-seq experiments using these annotations revealed several genes with caste-specific differential expression and tissue- or caste-specific splicing patterns that were missed in previous analyses. The extended 3' untranslated regions afforded great improvements in the analysis of existing single-cell RNA-seq data, resulting in the recovery of the transcriptomes of 18% more cells. The deeper single-cell transcriptomes obtained with these new annotations allowed us to identify additional markers for several cell types in the ant brain, as well as genes differentially expressed across castes in specific cell types.

CONCLUSIONS

Our results demonstrate that Iso-Seq is an efficient and effective approach to improve genome annotations and maximize the amount of information that can be obtained from existing and future genomic datasets in Harpegnathos and other organisms.

The Evolutionary Relevance of Social Learning and Transmission in Non-Social Arthropods with a Focus on Oviposition-Related Behaviors

Research on social learning has centered around vertebrates, but evidence is accumulating that small-brained, non-social arthropods also learn from others. Social learning can lead to social inheritance when socially acquired behaviors are transmitted to subsequent generations. Using oviposition site selection, a critical behavior for most arthropods, as an example, we first highlight the complementarities between social and classical genetic inheritance. We then discuss the relevance of studying social learning and transmission in non-social arthropods and document known cases in the literature, including examples of social learning from con- and hetero-specifics. We further highlight under which conditions social learning can be adaptive or not. We conclude that non-social arthropods and the study of oviposition behavior offer unparalleled opportunities to unravel the importance of social learning and inheritance for animal evolution.

Experimental psychology meets behavioral ecology: what laboratory studies of learning polymorphisms mean for learning under natural conditions, and vice versa

Behavior genetics, and specifically the study of learning and memory, has benefitted immensely from the development of powerful forward- and reverse-genetic methods for investigating the relationships between genes and behavior. Application of these methods in controlled laboratory settings has led to insights into gene-behavior relationships. In this perspective article, we argue that the field is now poised to make significant inroads into understanding the adaptive value of heritable variation in behavior in natural populations. Studies of natural variation with several species, in particular, are now in a position to complement laboratory studies of mechanisms, and sometimes this work can lead to counterintuitive insights into the mechanism of gene action on behavior. We make this case using a recent example from work with the honey bee, Apis mellifera.

Learning to collaborate: bringing together behavior and quantitative genomics

The genetic basis of complex trait like learning and memory have been well studied over the decades. Through those groundbreaking findings, we now have a better understanding about some of the genes and pathways that are involved in learning and/or memory. However, few of these findings identified the naturally segregating variants that are influencing learning and/or memory within populations. In this special issue honoring the legacy of Troy Zars, we review some of the traditional approaches that have been used to elucidate the genetic basis of learning and/or memory, specifically in fruit flies. We highlight some of his contributions to the field, and specifically describe his vision to bring together behavior and quantitative genomics with the aim of expanding our knowledge of the genetic basis of both learning and memory. Finally, we present some of our recent work in this area using a multiparental population (MPP) as a case study and describe the potential of this approach to advance our understanding of neurogenetics.

Finding a place and leaving a mark in memory formation

Preference for spatial locations to maximize favorable outcomes and minimize aversive experiences helps animals survive and adapt to the changing environment. Both visual and non-visual cues play a critical role in spatial navigation and memory of a place supports and guides these strategies. Here we present the neural, genetic and behavioral processes involved in place memory formation using Drosophila melanogaster with a focus on non-visual cue based spatial memories. The work presented here highlights the work done by Dr. Troy Zars and his colleagues with an emphasis on role of biogenic amines in learning, cell biological mechanisms of neural systems and behavioral plasticity of place conditioning.