Trait mapping in diverse arthropods by bulked segregant analysis

Kurlovs, Andre H.; Snoeck, Simon; Kosterlitz, Olivia; Leeuwen, Thomas Van; Clark, Richard M.

doi:10.1016/j.cois.2019.08.004

Cited by 38 publications

(43 citation statements)

References 70 publications

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“…This mirrors results in many other studies and may help to explain why diapause-mediated phenology is so evolutionarily pliable ( 8 , 9 , 82 – 84 ). Building on these results, the extreme phenotyping design of the current study yielded high statistical power ( 85 ), leading to high technical repeatability (independent GWA in each host race) of genotype-to-phenotype relationships for many loci, each with comparatively small effect. Moreover, signatures of genome-wide allelic divergence but not of hard selective sweeps were consistent with polygenic adaptation through soft sweeps ( 58 ).…”

Section: Discussionmentioning

confidence: 89%

Genome-wide variation and transcriptional changes in diverse developmental processes underlie the rapid evolution of seasonal adaptation

Dowle

Powell

Doellman

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Many organisms enter a dormant state in their life cycle to deal with predictable changes in environments over the course of a year. The timing of dormancy is therefore a key seasonal adaptation, and it evolves rapidly with changing environments. We tested the hypothesis that differences in the timing of seasonal activity are driven by differences in the rate of development during diapause in Rhagoletis pomonella, a fly specialized to feed on fruits of seasonally limited host plants. Transcriptomes from the central nervous system across a time series during diapause show consistent and progressive changes in transcripts participating in diverse developmental processes, despite a lack of gross morphological change. Moreover, population genomic analyses suggested that many genes of small effect enriched in developmental functional categories underlie variation in dormancy timing and overlap with gene sets associated with development rate in Drosophila melanogaster. Our transcriptional data also suggested that a recent evolutionary shift from a seasonally late to a seasonally early host plant drove more rapid development during diapause in the early fly population. Moreover, genetic variants that diverged during the evolutionary shift were also enriched in putative cis regulatory regions of genes differentially expressed during diapause development. Overall, our data suggest polygenic variation in the rate of developmental progression during diapause contributes to the evolution of seasonality in R. pomonella. We further discuss patterns that suggest hourglass-like developmental divergence early and late in diapause development and an important role for hub genes in the evolution of transcriptional divergence.

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Section: Discussionmentioning

confidence: 89%

Genome-wide variation and transcriptional changes in diverse developmental processes underlie the rapid evolution of seasonal adaptation

Dowle

Powell

Doellman

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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“…However, geneexpression patterns have shown to be complex and failed to clearly identify which cytochrome P450(s) might be involved. Future work should focus on trying to get functional data on pyflubumide metabolizing enzymes and characterize resistance with alternative hypothesis-free approaches such as QTL mapping (Kurlovs et al 2019). Table The toxicity was selected with cyenopyrafen resulting in JPR (Khalighi et al 2016) and developed low to moderate cross-resistance to pyflubumide.…”

Section: Discussionmentioning

confidence: 99%

Resistance risk assessment of the novel complex II inhibitor pyflubumide in the polyphagous pest Tetranychus urticae

et al. 2020

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Pyflubumide is a novel selective carboxanilide acaricide that inhibits mitochondrial complex II of mainly spider species such as Tetranychus urticae. We explored the baseline toxicity and potential crossresistance risk of pyflubumide in a reference panel of T. urticae strains resistant to various acaricides with different modes of action. A cyenopyrafen resistant strain (JPR) was identified as the only strain with low-to-moderate level of cross-resistance to pyflubumide (LC50 = 49.07 mg/L). In a resistance risk assessment approach, JPR was subsequently selected which lead to two highly resistant strains JPR-R1 (LC50 = 1437.48 mg/L) and JPR-R2 (LC50 = 1893.67 mg/L). Interestingly, compared to adult females, resistance was much less pronounced in adult males and eggs of the two JPR-R strains. In order to elucidate resistance mechanisms, we first sequenced complex II subunits in susceptible and resistant strains, but target-site insensitivity could not be detected. In contrast, synergism/ antagonism experiments strongly suggested that cytochrome P450 monooxygenases are involved in pyflubumide resistance. We therefore conducted genome-wide gene expression experiments to investigate constitutive and induced expression patterns and documented the overexpression of five cytochrome P450 and four CCE genes in JPR-Rs after pyflubumide exposure. Together, we provide a thorough resistance risk assessment of a novel complex II inhibitor, and provide first evidence for metabolic resistance mediated by cytochrome P450s in T. urticae.

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“…As revealed by recent studies, T. urticae is highly amenable to BSA genetic mapping, with QTL, including for quantitative pesticide resistance, narrowed to small genomic intervals that have suggested specific candidate genes and causal alleles [29,33]. In some instances, known causal variants were recovered [35–38], confirming the validity of the narrow genomic intervals identified by BSA studies using large, highly replicated T. urticae experimental populations [25].…”

Section: Introductionmentioning

confidence: 67%

“…To locate the genomic regions that underlie pyflubumide resistance in the pyflubumide-selected populations, we employed a bulked segregant analysis (BSA) approach using high-quality SNP loci [25,29]. Genome-wide JPR-R1 allele frequencies between pyflubumide-selected and susceptible (control) populations (Fig 4A ) and the matched pairs of populations (Fig 4B) revealed large deviations in allele frequencies on chromosomes 1 and 2.…”

Section: Genetic Mapping Uncovers Multiple Qtl Associated With Pyflubumide Selectionmentioning

confidence: 99%

High-resolution genetic mapping revealscis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pest

Fotoukkiaii

Wybouw

Kurlovs

et al. 2021

Preprint

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Chemical control strategies are driving the evolution of pesticide resistance in pest populations. Understanding the genetic mechanisms of these evolutionary processes is of crucial importance to develop sustainable resistance management strategies. The acaricide pyflubumide is one of the most recently developed mitochondrial complex II inhibitors with a new mode of action that specifically targets spider mite pests. In this study, we characterize the molecular basis of pyflubumide resistance in a highly resistant population of the spider mite Tetranychus urticae . Classical genetic crosses indicated that pyflubumide resistance was incompletely recessive and controlled by more than one gene. To identify resistance loci, we crossed the resistant population to a highly susceptible T. urticae inbred strain and propagated resulting populations with and without pyflubumide exposure for multiple generations in an experimental evolution set-up. High-resolution genetic mapping by a bulked segregant analysis approach led to the identification of three quantitative trait loci (QTL) linked to pyflubumide resistance. Two QTLs were found on the first chromosome and centered on the cytochrome P450 CYP392A16 and a cluster of CYP392E6-8 genes. Comparative transcriptomics revealed a consistent overexpression of CYP392A16 and CYP392E8 in the experimental populations that were selected for pyflubumide resistance. We further corroborated the involvement of CYP392A16 in resistance by in vitro functional expression and metabolism studies. Collectively, these experiments uncovered that CYP392A16 N-demethylates the toxic carboxamide form of pyflubumide to a non-toxic compound . A third QTL coincided with cytochrome P450 reductase ( CPR ), a vital component of cytochrome P450 metabolism. We show here that the resistant population harbors three gene copies of CPR and that this copy number variation is associated with higher mRNA abundance . Together, we provide evidence for detoxification of pyflubumide by cytochrome P450s that is likely synergized by gene amplification of CPR .

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Trait mapping in diverse arthropods by bulked segregant analysis

Cited by 38 publications

References 70 publications

Genome-wide variation and transcriptional changes in diverse developmental processes underlie the rapid evolution of seasonal adaptation

Genome-wide variation and transcriptional changes in diverse developmental processes underlie the rapid evolution of seasonal adaptation

Resistance risk assessment of the novel complex II inhibitor pyflubumide in the polyphagous pest Tetranychus urticae

High-resolution genetic mapping revealscis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pest

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