scholarly journals Spatiotemporal patterns of desiccation tolerance in natural populations of Drosophila melanogaster

2016 ◽  
Author(s):  
Subhash Rajpurohit ◽  
Eran Gefen ◽  
Alan Bergland ◽  
Dmitri Petrov ◽  
Allen G Gibbs ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Drought Tolerance ◽  
North American ◽  
Desiccation Tolerance ◽  
Experimental Evolution ◽  
Association Studies ◽  
Natural Populations ◽  
Genome Wide Association Studies ◽  
Physiological Basis ◽  
Genome Wide

AbstractWater availability is a major environmental challenge to a variety of terrestrial organisms. In insects, desiccation tolerance varies predictably over various spatial and temporal scales and is an important physiological basis of fitness variation among natural populations. Here, we examine the dynamics of desiccation tolerance in North American populations of Drosophila melanogaster using: 1) natural populations sampled across latitudes and seasons in the eastern USA; 2) experimental evolution in the field in response to changing seasonal environments; 3) a sequenced panel of inbred lines (DGRP) to perform genome wide associations and examine whether SNPs/genes associated with variation in desiccation tolerance exhibit patterns of clinal and/or seasonal enrichment in pooled sequencing of populations. In natural populations we observed a shallow cline in desiccation tolerance, for which tolerance exhibited a positive association with latitude; the steepness of this cline increased with decreasing culture temperature, demonstrating a significant degree of thermal plasticity. No differences in desiccation tolerance were observed between spring and autumn collections from three mid-to-northern latitude populations, or as a function of experimental evolution to seasonality. Similarly, water loss rates did not vary significantly among latitudinal, seasonal or experimental evolution populations. However, changes in metabolic rates during prolonged exposure to dry conditions indicate increased tolerance in higher latitude populations. Genome wide association studies identified thirty-six SNPs in twenty-eight genes associated with sex-averaged drought tolerance. Among North American populations, genes associated with drought tolerance do not show increased signatures of spatially varying selection relative to the rest of the genome, whereas among Australian populations they do.

scholarly journals Cis and trans-acting variants contribute to survivorship in a naïve Drosophila melanogaster population exposed to ryanoid insecticides

2018 ◽  
Author(s):  
Llewellyn Green ◽  
Paul Battlay ◽  
Alexandre Fournier-Level ◽  
Robert T. Good ◽  
Charles Robin
Keyword(s):  
Drosophila Melanogaster ◽  
Insecticide Resistance ◽  
Allelic Variation ◽  
Association Studies ◽  
Natural Populations ◽  
Intermediate Frequency ◽  
Genome Wide Association ◽  
Systems Genetics ◽  
Genome Wide Association Studies ◽  
Genome Wide

AbstractInsecticide resistance is a paradigm of microevolution and insecticides are responsible for the strongest cases of recent selection in the genome of Drosophila melanogaster. Here we use a naïve population and a novel insecticide class to examine the ab initio genetic architecture of a potential selective response. Genome wide association studies of chlorantraniliprole susceptibility reveal variation in a gene of major effect, Stretchin Myosin light chain kinase (Strn-Mlck), which we validate with linkage mapping and transgenic manipulation of gene expression. We propose that allelic variation in Strn-Mlck alters sensitivity to the calcium depletion attributable to chlorantraniliprole’s mode of action. Genome-wide association studies also reveal a network of genes involved in neuromuscular biology. In contrast, phenotype to transcriptome associations identify differences in constitutive levels of multiple transcripts regulated by cnc, the homologue of mammalian Nrf2. This suggests that genetic variation acts in trans to regulate multiple metabolic enzymes in this pathway. The most outstanding association is with the transcription level of Cyp12d1 which is also affected in cis by copy number variation. Transgenic overexpression of Cyp12d1 reduces susceptibility to both chlorantraniliprole and the closely related insecticide cyantraniliprole. This systems genetics study reveals multiple allelic variants segregating at intermediate frequency in a population that is completely naïve to this new insecticide chemistry and it adumbrates a selective response among natural populations to these chemicals.SignificanceAround the world insecticides are being deregistered and banned, as their environmental costs are deemed too great or their efficacy against pest insects is reduced through the evolution of insecticide resistance. With the introduction of replacement insecticides comes the responsibility to assess the way new insecticides perturb various levels of biological systems; from insect physiology to ecosystems. We used a systems genetics approach to identify genetic variants affecting survivorship of Drosophila melanogaster exposed to chlorantraniliprole. The study population was completely naïve to this insecticide chemistry and yet we find associations with variants in neuromuscular genes and co-regulated detoxification genes. We predict that these variants will increase in populations of this ‘sentinel species’ as these insecticides are applied in the environment.

Identifying toxin-targets through experimental evolution and genome-wide association studies

Toxicon ◽  
2020 ◽  
Vol 182 ◽  
pp. S11
Author(s):  
M.J. Ward ◽  
S.A. Ellsworth ◽  
D.R. Rokyta
Keyword(s):  
Experimental Evolution ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals Structural variants and selective sweep foci contribute to insecticide resistance in the Drosophila melanogaster genetic reference panel

2018 ◽  
Author(s):  
Paul Battlay ◽  
Llewellyn Green ◽  
Pontus B. Leblanc ◽  
Joshua M. Schmidt ◽  
Alexandre Fournier-Level ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Element ◽  
Selective Sweep ◽  
Association Studies ◽  
Transcript Abundance ◽  
Reference Panel ◽  
Drosophila Genome ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Number Variation

AbstractPatterns of nucleotide polymorphism within populations of Drosophila melanogaster suggest that insecticides have been the selective agents driving the strongest recent bouts of positive selection. However, there is a need to explicitly link selective sweep loci to the particular insecticide phenotypes that could plausibly account for the drastic selective responses that are observed in these non-target insects. Here, we screen the Drosophila Genetic Reference Panel with two common insecticides; malathion (an organophosphate) and permethrin (a pyrethroid). Genome wide association studies map ‘survival-on-malathion’ to two of the largest sweeps in the D. melanogaster genome; Ace and Cyp6g1. Malathion survivorship also correlates with lines which have high levels of Cyp12d1 and Jheh1 and Jheh2 transcript abundance. Permethrin phenotypes map to the largest cluster of P450 genes in the Drosophila genome, however in contrast to a selective sweep driven by insecticide use, the derived state seems to be associated with susceptibility. These results underscore previous findings that highlight the importance of structural variation to insecticide phenotypes: Cyp6g1 exhibits copy number variation and transposable element insertions, Cyp12d1 is tandemly duplicated, the Jheh loci are associated with a Bari1 transposable element insertion, and a Cyp6a17 deletion is associated with susceptibility.

scholarly journals The power of a multivariate approach to genome-wide association studies: an example with Drosophila melanogaster wing shape

2017 ◽  
Author(s):  
William Pitchers ◽  
Jessica Nye ◽  
Eladio J. Márquez ◽  
Alycia Kowalski ◽  
Ian Dworkin ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Multivariate Analyses ◽  
Association Studies ◽  
Significant Snps ◽  
Wing Shape ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Phenotypic Effect ◽  
Genome Wide ◽  
Univariate Analyses

AbstractDue to the complexity of genotype-phenotype relationships, simultaneous analyses of genomic associations with multiple traits will be more powerful and more informative than a series of univariate analyses. In most cases, however, studies of genotype-phenotype relationships have analyzed only one trait at a time, even as the rapid advances in molecular tools have expanded our view of the genotype to include whole genomes. Here, we report the results of a fully integrated multivariate genome-wide association analysis of the shape of the Drosophila melanogaster wing in the Drosophila Genetic Reference Panel. Genotypic effects on wing shape were highly correlated between two different labs. We found 2,396 significant SNPs using a 5% FDR cutoff in the multivariate analyses, but just 4 significant SNPs in univariate analyses of scores on the first 20 principal component axes. A key advantage of multivariate analysis is that the direction of the estimated phenotypic effect is much more informative than a univariate one. Exploiting this feature, we show that the directions of effects were on average replicable in an unrelated panel of inbred lines. Effects of knockdowns of genes implicated in the initial screen were on average more similar than expected under a null model. Association studies that take a phenomic approach in considering many traits simultaneously are an important complement to the power of genomics. Multivariate analyses of such data are more powerful, more informative, and allow the unbiased study of pleiotropy.

scholarly journals Ecophysiological genomics identifies a pleiotropic locus mediating drought tolerance in sorghum

2021 ◽  
Author(s):  
Fanna Maina ◽  
Abdou Harou ◽  
Falalou Hamidou ◽  
Geoffrey P. Morris
Keyword(s):  
Drought Tolerance ◽  
Water Use ◽  
Yield Components ◽  
Association Studies ◽  
Experimental System ◽  
Grain Weight ◽  
Phenotypic Variance ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Vegetative Biomass

ABSTRACTDrought is a key constraint on plant productivity and threat to food security. Sorghum (Sorghum bicolor L. Moench), a global staple food and forage crop, is among the most drought-adapted cereal crops, but its adaptation is not yet well understood. This study aims to better understand the genetic basis of preflowering drought in sorghum and identify loci underlying variation in water use and yield components under drought. A panel of 219 diverse sorghum from West Africa was phenotyped for yield components and water use in an outdoor large-tube lysimeter system under well-watered (WW) versus a preflowering drought water-stressed (WS) treatment. The experimental system was validated based on characteristic drought response in international drought tolerance check genotypes and genome-wide association studies (GWAS) that mapped the major height locus at QHT7.1 and Dw3. GWAS further identified marker trait associations (MTAs) for drought-related traits (plant height, flowering time, forage biomass, grain weight, water use) that each explained 7–70% of phenotypic variance. Most MTAs for drought-related traits correspond to loci not previously reported, but some MTA for forage biomass and grain weight under WS co-localized with staygreen post-flowering drought tolerance loci (Stg3a and Stg4). A globally common allele at S7_50055849 is associated with several yield components under drought, suggesting that it tags a major pleiotropic variant controlling assimilate partitioning to grain versus vegetative biomass. The GWAS findings revealed oligogenic variants for drought tolerance in sorghum landraces which could be used as trait predictive markers for improved drought adaptation.

scholarly journals Genomic architecture of biomass heterosis inArabidopsis

2017 ◽  
Vol 114 (30) ◽  
pp. 8101-8106 ◽  
Author(s):  
Mei Yang ◽  
Xuncheng Wang ◽  
Diqiu Ren ◽  
Hao Huang ◽  
Miqi Xu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Association Studies ◽  
Expression Patterns ◽  
Natural Populations ◽  
Genome Wide Association Studies ◽  
Genomic Architecture ◽  
Genome Wide ◽  
Stimulus Responsive ◽  
Abiotic Stimuli

Heterosis is most frequently manifested by the substantially increased vigorous growth of hybrids compared with their parents. Investigating genomic variations in natural populations is essential to understand the initial molecular mechanisms underlying heterosis in plants. Here, we characterized the genomic architecture associated with biomass heterosis in 200Arabidopsishybrids. The genome-wide heterozygosity of hybrids makes a limited contribution to biomass heterosis, and no locus shows an obvious overdominance effect in hybrids. However, the accumulation of significant genetic loci identified in genome-wide association studies (GWAS) in hybrids strongly correlates with better-parent heterosis (BPH). Candidate genes for biomass BPH fall into diverse biological functions, including cellular, metabolic, and developmental processes and stimulus-responsive pathways. Important heterosis candidates includeWUSCHEL,ARGOS, and some genes that encode key factors involved in cell cycle regulation. Interestingly, transcriptomic analyses in representativeArabidopsishybrid combinations reveal that heterosis candidate genes are functionally enriched in stimulus-responsive pathways, including responses to biotic and abiotic stimuli and immune responses. In addition, stimulus-responsive genes are repressed to low-parent levels in hybrids with high BPH, whereas middle-parent expression patterns are exhibited in hybrids with no BPH. Our study reveals a genomic architecture for understanding the molecular mechanisms of biomass heterosis inArabidopsis, in which the accumulation of the superior alleles of genes involved in metabolic and cellular processes improve the development and growth of hybrids, whereas the overall repressed expression of stimulus-responsive genes prioritizes growth over responding to environmental stimuli in hybrids under normal conditions.

scholarly journals Increasing the power of genome wide association studies in natural populations using repeated measures – evaluation and implementation

2016 ◽  
Vol 7 (7) ◽  
pp. 792-799 ◽  
Author(s):  
Lars Rönnegård ◽  
S. Eryn McFarlane ◽  
Arild Husby ◽  
Takeshi Kawakami ◽  
Hans Ellegren ◽  
...  
Keyword(s):  
Repeated Measures ◽  
Association Studies ◽  
Natural Populations ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals Accurate, ultra-low coverage genome reconstruction and association studies in Hybrid Swarm mapping populations

2021 ◽  
Vol 11 (4) ◽  
Author(s):  
Cory A Weller ◽  
Susanne Tilk ◽  
Subhash Rajpurohit ◽  
Alan O Bergland
Keyword(s):  
Genetic Variation ◽  
Sequence Data ◽  
Association Studies ◽  
Recombinant Inbred Lines ◽  
Natural Populations ◽  
Inbred Lines ◽  
Genome Wide Association Studies ◽  
Hybrid Swarm ◽  
Genome Wide ◽  
Low Coverage

Abstract Genetic association studies seek to uncover the link between genotype and phenotype, and often utilize inbred reference panels as a replicable source of genetic variation. However, inbred reference panels can differ substantially from wild populations in their genotypic distribution, patterns of linkage-disequilibrium, and nucleotide diversity. As a result, associations discovered using inbred reference panels may not reflect the genetic basis of phenotypic variation in natural populations. To address this problem, we evaluated a mapping population design where dozens to hundreds of inbred lines are outbred for few generations, which we call the Hybrid Swarm. The Hybrid Swarm approach has likely remained underutilized relative to pre-sequenced inbred lines due to the costs of genome-wide genotyping. To reduce sequencing costs and make the Hybrid Swarm approach feasible, we developed a computational pipeline that reconstructs accurate whole genomes from ultra-low-coverage (0.05X) sequence data in Hybrid Swarm populations derived from ancestors with phased haplotypes. We evaluate reconstructions using genetic variation from the Drosophila Genetic Reference Panel as well as variation from neutral simulations. We compared the power and precision of Genome-Wide Association Studies using the Hybrid Swarm, inbred lines, recombinant inbred lines (RILs), and highly outbred populations across a range of allele frequencies, effect sizes, and genetic architectures. Our simulations show that these different mapping panels vary in their power and precision, largely depending on the architecture of the trait. The Hybrid Swam and RILs outperform inbred lines for quantitative traits, but not for monogenic ones. Taken together, our results demonstrate the feasibility of the Hybrid Swarm as a cost-effective method of fine-scale genetic mapping.

scholarly journals Cross-Species association statistics for genome-wide studies of host and parasite polymorphism data

2019 ◽  
Author(s):  
Hanna Märkle ◽  
Aurélien Tellier ◽  
Sona John
Keyword(s):  
Statistical Power ◽  
Association Studies ◽  
Natural Populations ◽  
Genomic Data ◽  
Genome Wide Association Studies ◽  
Full Genome ◽  
Species Association ◽  
Genome Data ◽  
Genome Wide ◽  
The Cross

AbstractUncovering the genes governing host-parasite coevolution is of importance for disease management in agriculture and human medicine. The availability of increasing amounts of host and parasite full genome-data in recent times allows to perform cross-species genome-wide association studies based on sampling of genomic data of infected hosts and their associated parasites strains. We aim to understand the statistical power of such approaches. We develop two indices, the cross species association (CSA) and the cross species prevalence (CSP), the latter additionally incorporating genomic data from uninfected hosts. For both indices, we derive genome-wide significance thresholds by computing their expected distribution over unlinked neutral loci, i.e. those not involved in determining the outcome of interaction. Using a population genetics and an epidemiological coevolutionary model, we demonstrate that the statistical power of these indices to pinpoint the interacting loci in full genome data varies over time. This is due to the underlying GxG interactions and the coevolutionary dynamics. Under trench-warfare dynamics, CSA and CSP are very accurate in finding out the loci under coevolution, while under arms-race dynamics the power is limited especially under a gene-for-gene interaction. Furthermore, we reveal that the combination of both indices across time samples can be used to estimate the asymmetry of the underlying infection matrix. Our results provide novel insights into the power and biological interpretation of cross-species association studies using samples from natural populations or controlled experiments.

scholarly journals Genetic Dissection of Seedling Root System Architectural Traits in a Diverse Panel of Hexaploid Wheat through Multi-Locus Genome-Wide Association Mapping for Improving Drought Tolerance

2021 ◽  
Vol 22 (13) ◽  
pp. 7188
Author(s):  
T. Danakumara ◽  
Jyoti Kumari ◽  
Amit Kumar Singh ◽  
Subodh Kumar Sinha ◽  
Anjan Kumar Pradhan ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Root Length Density ◽  
Association Studies ◽  
Average Diameter ◽  
Genome Wide Association ◽  
Phenotypic Variance ◽  
Genome Wide Association Studies ◽  
Association Panel ◽  
Genome Wide ◽  
Genomic Regions

Cultivars with efficient root systems play a major role in enhancing resource use efficiency, particularly water absorption, and thus in drought tolerance. In this study, a diverse wheat association panel of 136 wheat accessions including mini core subset was genotyped using Axiom 35k Breeders’ Array to identify genomic regions associated with seedling stage root architecture and shoot traits using multi-locus genome-wide association studies (ML-GWAS). The association panel revealed a wide variation of 1.5- to 50- fold and were grouped into six clusters based on 15 traits. Six different ML-GWAS models revealed 456 significant quantitative trait nucleotides (QTNs) for various traits with phenotypic variance in the range of 0.12–38.60%. Of these, 87 QTNs were repeatedly detected by two or more models and were considered reliable genomic regions for the respective traits. Among these QTNs, eleven were associated with average diameter and nine each for second order lateral root number (SOLRN), root volume (RV) and root length density (RLD). A total of eleven genomic regions were pleiotropic and each controlled two or three traits. Some important candidate genes such as Formin homology 1, Ubiquitin-like domain superfamily and ATP-dependent 6-phosphofructokinase were identified from the associated genomic regions. The genomic regions/genes identified in this study could potentially be targeted for improving root traits and drought tolerance in wheat.

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