Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations ofPopulus trichocarpa

Understanding the genomic and environmental basis of cold adaptation is key to understand how plants survive and adapt to different environmental conditions across their natural range. Univariate and multivariate genome-wide association (GWAS) and genotype-environment association (GEA) analyses were used to test associations among genome-wide SNPs obtained from whole-genome resequencing, measures of growth, phenology, emergence, cold hardiness, and range-wide environmental variation in coastal Douglas-fir (Pseudotsuga menziesii). Results suggest a complex genomic architecture of cold adaptation, in which traits are either highly polygenic or controlled by both large and small effect genes. Newly discovered associations for cold adaptation in Douglas-fir included 130 genes involved in many important biological functions such as primary and secondary metabolism, growth and reproductive development, transcription regulation, stress and signaling, and DNA processes. These genes were related to growth, phenology and cold hardiness and strongly depend on variation in environmental variables such degree days below 0c, precipitation, elevation and distance from the coast. This study is a step forward in our understanding of the complex interconnection between environment and genomics and their role in cold-associated trait variation in boreal tree species, providing a baseline for the species’ predictions under climate change.

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Evaluating the power and limitations of genome-wide association mapping in C. elegans

10.1101/2021.09.09.459688 ◽

2021 ◽

Author(s):

Samuel J. Widmayer ◽

Kathryn S. Evans ◽

Stefan Zdraljevic ◽

Erik C. Andersen

Keyword(s):

Quantitative Trait ◽

Complex Traits ◽

Genetic Basis ◽

Natural Populations ◽

Evolutionary Genetics ◽

Genome Wide Association ◽

C Elegans ◽

Quantitative Genetic ◽

Genome Wide ◽

Simulation Based

A central goal of evolutionary genetics in Caenorhabditis elegans is to understand the genetic basis of traits that contribute to adaptation and fitness. Genome-wide association (GWA) mappings scan the genome for individual genetic variants that are significantly correlated with phenotypic variation in a population, or quantitative trait loci (QTL). GWA mappings are a popular choice for quantitative genetic analyses because the QTL that are discovered segregate in natural populations. Despite numerous successful mapping experiments, the empirical performance of GWA mappings has not, to date, been formally evaluated for this species. We developed an open-source GWA mapping pipeline called NemaScan and used a simulation-based approach to provide benchmarks of mapping performance among wild C. elegans strains. Simulated trait heritability and complexity determined the spectrum of QTL detected by GWA mappings. Power to detect smaller-effect QTL increased with the number of strains sampled from the C. elegans Natural Diversity Resource (CeNDR). Population structure was a major driver of variation in GWA mapping performance, with populations shaped by recent selection exhibiting significantly lower false discovery rates than populations composed of more divergent strains. We also recapitulated previous GWA mappings of experimentally validated quantitative trait variants. Our simulation-based evaluation of GWA performance provides the community with critical context for pursuing quantitative genetic studies using CeNDR to elucidate the genetic basis of complex traits in C. elegans natural populations.

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Population structure of the Brachypodium species complex and genome wide association of agronomic traits in response to climate

10.1101/246074 ◽

2018 ◽

Cited By ~ 1

Author(s):

Pip Wilson ◽

Jared Streich ◽

Kevin Murray ◽

Steve Eichten ◽

Riyan Cheng ◽

...

Keyword(s):

Species Complex ◽

Agronomic Traits ◽

Association Studies ◽

Genomic Structure ◽

Natural Populations ◽

Climatic Conditions ◽

Model Systems ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide

AbstractThe development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translational to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and sequenced using genotyping by sequencing (GBS). Overall, 1,897 samples were classified into two diploid or allopolyploid species and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines were selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22 and 47 QTLs were identified for flowering time, early vigour and energy traits, respectively. Overall, the results highlight the genomic structure of the Brachypodium species complex and allow powerful complex trait dissection within this new grass model species.

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The genetic basis of cooperation and conflict in natural populations of a model symbiont

10.1101/2021.07.19.452989 ◽

2021 ◽

Author(s):

Rebecca T Batstone ◽

Liana T Burghardt ◽

Katy D Heath

Keyword(s):

Nucleotide Diversity ◽

Genetic Basis ◽

Balancing Selection ◽

Association Studies ◽

Natural Populations ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Ensifer Meliloti ◽

Single Versus

Although mutualisms are defined as net beneficial interactions among species, whether fitness conflict or alignment drive the evolution of these interactions is unclear. Examining the relationships between host and symbiont fitness proxies at both the organismal and genomic levels can provide new insights. Here, we utilized data from several genome-wide association studies (GWAS) that involved 191 strains of the N-fixing rhizobium symbiont, Ensifer meliloti, collected from natural populations being paired in single or mixed inoculation with two genotypes of the host Medicago truncatula to determine how different proxies of microbial fitness were related to one another, and examine signatures of fitness conflict and alignment between host and symbiont at both the whole-organism and genomic levels. We found little evidence for fitness conflict; instead, loci tended to have concordant effects on both host and symbiont fitness and showed heightened nucleotide diversity and signatures of balancing selection compared to the rest of the genome. We additionally found that single versus competitive measures of rhizobium fitness are distinct, and that the latter should be used given that they better reflect the ecological conditions rhizobia experience in nature. Our results suggest that although conflict appears to be largely resolved in natural populations of rhizobia, mutualistic coevolution between legumes and rhizobia can nonetheless maintain genetic diversity, potentially explaining why variation in symbiotic traits persists in nature.

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

10.1101/502161 ◽

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.

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Distinct characteristics of genes associated with phenome-wide variation in maize (Zea mays)

10.1101/534503 ◽

2019 ◽

Cited By ~ 2

Author(s):

Zhikai Liang ◽

Yumou Qiu ◽

James C. Schnable

Keyword(s):

Natural Populations ◽

Purifying Selection ◽

Forward Genetics ◽

Genome Wide Association ◽

Phenotypic Traits ◽

Functional Variation ◽

Maize Diversity ◽

Genome Wide ◽

Gene Models ◽

Using Data

ABSTRACTNaturally occurring functionally variable alleles in specific genes within a population allows the identification of which genes are involved in the determination of which phenotypes. The omnigenetic model proposes that essentially all genes which are expressed in relevant contexts likely play some role in determining phenotypic outcomes. Here, we develop an approach to identify genes where natural functional variation plays a role in shaping many phenotypic traits simultaneously. We demonstrate that this approach identifies a distinct set of genes relative to conventional genome wide association using data for 260 traits scored a maize diversity panel, and the genes identified using this approach are more likely to be independently validated than genes identified by convetional genome wide association. Genes identified by the new approach share a number of features with a gold standard set of genes characterized through forward genetics which separate them from both genes identified by conventional genome wide association and the overall population of annotated gene models. These features include evidence of significantly stronger purifying selection, positional conservation across the genomes of related species, greater length, and a scarcity of presence absence variation for these loci in natural populations. Genes identified by phenome-wide analyses also showed much stronger signals of GO enrichment and purification than genes identified by conventional genome wide association. Overall these findings are consistent with large subset of annotated gene models – despite support from transcriptional and homology evidence – being unlikely to play any role in determining organismal phenotypes.

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