ALEXANDRE FOURNIER-LEVEL

Genome assembly of an Australian native grass species reveals a recent whole-genome duplication and biased gene retention of genes involved in stress response

Publisher: Oxford University Press (OUP)

Date: 28-12-2022

DOI: 10.1093/GIGASCIENCE/GIAD034

Abstract: The adaptive significance of polyploidy has been extensively debated, and chromosome-level genome assemblies of polyploids can provide insight into this. The Australian grass Bothriochloa decipiens belongs to the BCD clade, a group with a complex history of hybridization and polyploid. This is the first genome assembly and annotation of a species that belongs to this fascinating yet complex group. Using Illumina short reads, 10X Genomics linked reads, and Hi-C sequencing data, we assembled a highly contiguous genome of B. decipiens, with a total length of 1,218.22 Mb and scaffold N50 of 42.637 Mb. Comparative analysis revealed that the species experienced a relatively recent whole-genome duplication. We clustered the 20 major scaffolds, representing the 20 chromosomes, into the 2 subgenomes of the parental species using unique repeat signatures. We found evidence of biased fractionation and differences in the activity of transposable elements between the subgenomes prior to hybridization. Duplicates were enriched for genes involved in transcription and response to external stimuli, supporting a biased retention of duplicated genes following whole-genome duplication. Our results support the hypotheses of a biased retention of duplicated genes following polyploidy and point to differences in repeat activity associated with subgenome dominance. B. decipiens is a widespread species with the ability to establish across many soil types, making it a prime candidate for climate change– resilient ecological restoration of Australian grasslands. This reference genome is a valuable resource for future population genomic research on Australian grasses.

Evolution of the VvMybA gene family, the major determinant of berry colour in cultivated grapevine (Vitis vinifera L.)

Publisher: Springer Science and Business Media LLC

Date: 18-11-2009

DOI: 10.1038/HDY.2009.148

Abstract: Polymorphisms in the grape transcription factor family VvMybA are responsible for variation in anthocyanin content in the berries of cultivated grapevine (Vitis vinifera L. subsp. sativa). Previous study has shown that white grapes arose through the mutation of two adjacent genes: a retroelement insertion in VvMybA1 and a single-nucleotide polymorphism mutation in VvMybA2. The purpose of this study was to understand how these mutations emerged and affected genetic ersity at neighbouring sites and how they structured the genetic ersity of cultivated grapevines. We sequenced a total of 3225 bp of these genes in a core collection of genetic resources, and carried out empirical selection tests, phylogenetic- and coalescence-based demographic analyses. The insertion in the VvMybA1 promoter was shown to have occurred recently, after the mutation of VvMybA2, both mutations followed by a selective sweep. The mutational pattern for these colour genes is consistent with progressively relaxed selection from constrained ancestral coloured haplotypes to light coloured and finally white haplotypes. Dynamics of population size in the VvMybA genes showed an initial exponential growth, followed by population size stabilization. Most ancestral haplotypes are found in cultivars from western region, whereas recent haplotypes are essentially present in table cultivars from eastern regions where intense breeding practices may have replaced the original ersity. Finally, the emergence of the white allele was followed by a recent strong exponential growth, showing a very fast diffusion of the initial white allele.

Assessing the invasive potential of different source populations of ragweed (Ambrosia artemisiifolia L.) through genomically-informed species distribution modelling

Publisher: Authorea, Inc.

Date: 18-05-2023

DOI: 10.22541/AU.168440414.43686837/V1

Abstract: The genetic composition of founding populations plays a key role in determining invasion success. Despite this fact, the role of genetic variation on the potential distribution of invaders has rarely been investigated. Here, we integrate genomic data into ecological niche models (ENMs) to predict the distribution of globally invasive common ragweed (Ambrosia artemisiifolia) to Australia. We identified three genetic clusters of ragweed and used these clusters to construct separate ENMs. The predicted distribution of ragweed in Australia changed depending on the genetic composition and continent of origin of the source population. By quantifying this change, we identified source populations most likely to expand the ragweed distribution. As prevention remains the most effective method of invasive species management, our work provides a valuable way of ranking the threat posed by different populations to better inform management decisions.

compare_genomes: a comparative genomics workflow to streamline the analysis of evolutionary divergence across genomes

Publisher: Cold Spring Harbor Laboratory

Date: 17-03-2023

DOI: 10.1101/2023.03.16.533049

Abstract: The dawn of cost-effective genome assembly is enabling deep comparative genomics to address fundamental evolutionary questions by comparing the genomes of multiple species. However, comparative genomics analyses often deploy multiple, often purpose-built frameworks, limiting their transferability and replicability. Here, we developed compare_genomes, a transferable and extensible comparative genomics workflow package which streamlines the identification of orthologous families within and across genomes and tests for the presence of several mechanisms of evolution (gene family expansion or contraction and substitution rates within protein-coding sequences).

Dissecting genetic architecture of grape proanthocyanidin composition through quantitative trait locus mapping

Publisher: Springer Science and Business Media LLC

Date: 27-02-2012

DOI: 10.1186/1471-2229-12-30

Abstract: Proanthocyanidins (PAs), or condensed tannins, are flavonoid polymers, widespread throughout the plant kingdom, which provide protection against herbivores while conferring organoleptic and nutritive values to plant-derived foods, such as wine. However, the genetic basis of qualitative and quantitative PA composition variation is still poorly understood. To elucidate the genetic architecture of the complex grape PA composition, we first carried out quantitative trait locus (QTL) analysis on a 191-in idual pseudo-F1 progeny. Three categories of PA variables were assessed: total content, percentages of constitutive subunits and composite ratio variables. For nine functional candidate genes, among which eight co-located with QTLs, we performed association analyses using a ersity panel of 141 grapevine cultivars in order to identify causal SNPs. Multiple QTL analysis revealed a total of 103 and 43 QTLs, respectively for seed and skin PA variables. Loci were mainly of additive effect while some loci were primarily of dominant effect. Results also showed a large involvement of pairwise epistatic interactions in shaping PA composition. QTLs for PA variables in skin and seeds differed in number, position, involvement of epistatic interaction and allelic effect, thus revealing different genetic determinisms for grape PA composition in seeds and skin. Association results were consistent with QTL analyses in most cases: four out of nine tested candidate genes ( VvLAR1 , VvMYBPA2 , VvCHI1 , VvMYBPA1 ) showed at least one significant association with PA variables, especially VvLAR1 revealed as of great interest for further functional investigation. Some SNP-phenotype associations were observed only in the ersity panel. This study presents the first QTL analysis on grape berry PA composition with a comparison between skin and seeds, together with an association study. Our results suggest a complex genetic control for PA traits and different genetic architectures for grape PA composition between berry skin and seeds. This work also uncovers novel genomic regions for further investigation in order to increase our knowledge of the genetic basis of PA composition.

Herbicide resistance costs: what are we actually measuring and why?

Publisher: Wiley

Date: 26-02-2018

DOI: 10.1002/PS.4819

Abstract: Despite the considerable research efforts invested over the years to measure the fitness costs of herbicide resistance, these have rarely been used to inform a predictive theory about the fate of resistance once the herbicide is discontinued. One reason for this may be the reductive focus on relative fitness of two genotypes as a single measure of differential performance. Although the extent of variation in relative fitness between resistant and susceptible plants has not been assessed consistently, we know enough about plant physiology and ecology not to reduce it to a single fixed value. Research must therefore consider carefully the relevance of the experimental environment, the life stage and the choice of metric when measuring fitness-related traits. The reason most often given for measuring the cost of resistance, prediction of the impacts of management options on population dynamics, cannot be addressed using arbitrary components of fitness or a fixed value of relative fitness. To inform management options, the measurement of traits that capture the relevant processes and the main causes of their variation are required. With an emphasis on the benefit of field experiments measured over multiple time points and seasons, we highlight ex les of studies that have made significant advances in this direction. © 2017 Society of Chemical Industry.

Repeated local emergence of carbapenem-resistant Acinetobacter baumannii in a single hospital ward

Publisher: Microbiology Society

Date: 02-03-2016

DOI: 10.1099/MGEN.0.000050

Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine

Publisher: Public Library of Science (PLoS)

Date: 03-11-2014

DOI: 10.1371/JOURNAL.PONE.0110436

Cisandtrans-acting variants contribute to survivorship in a naïveDrosophila melanogasterpopulation exposed to ryanoid insecticides

Publisher: Cold Spring Harbor Laboratory

Date: 20-12-2018

DOI: 10.1101/502161

Abstract: Insecticide 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. Around 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.

Optimizing sampling design and sequencing strategy for the genomic analysis of quantitative traits in natural populations

Publisher: Wiley

Date: 16-07-2021

DOI: 10.1111/1755-0998.13458

Abstract: Mapping the genes underlying ecologically relevant traits in natural populations is fundamental to develop a molecular understanding of species adaptation. Current sequencing technologies enable the characterization of a species’ genetic ersity across the landscape or even over its whole range. The relevant capture of the genetic ersity across the landscape is critical for a successful genetic mapping of traits and there are no clear guidelines on how to achieve an optimal s ling and which sequencing strategy to implement. Here we determine, through simulation, the s ling scheme that maximizes the power to map the genetic basis of a complex trait in an outbreeding species across an idealized landscape and draw genomic predictions for the trait, comparing in idual and pool sequencing strategies. Our results show that quantitative trait locus detection power and prediction accuracy are higher when more populations over the landscape are s led and this is more cost‐effectively done with pool sequencing than with in idual sequencing. Additionally, we recommend s ling populations from areas of high genetic ersity. As progress in sequencing enables the integration of trait‐based functional ecology into landscape genomics studies, these findings will guide study designs allowing direct measures of genetic effects in natural populations across the environment.

Haplotype diversity of VvTFL1A gene and association with cluster traits ingrapevine (V. vinifera)

Publisher: Springer Science and Business Media LLC

Date: 05-08-2014

DOI: 10.1186/S12870-014-0209-3

Quantitative Genetic Bases of Anthocyanin Variation in Grape (Vitis vinifera L. ssp. sativa) Berry: A Quantitative Trait Locus to Quantitative Trait Nucleotide Integrated Study

Publisher: Oxford University Press (OUP)

Date: 11-2009

DOI: 10.1534/GENETICS.109.103929

Abstract: The combination of QTL mapping studies of synthetic lines and association mapping studies of natural ersity represents an opportunity to throw light on the genetically based variation of quantitative traits. With the positional information provided through quantitative trait locus (QTL) mapping, which often leads to wide intervals encompassing numerous genes, it is now feasible to directly target candidate genes that are likely to be responsible for the observed variation in completely sequenced genomes and to test their effects through association genetics. This approach was performed in grape, a newly sequenced genome, to decipher the genetic architecture of anthocyanin content. Grapes may be either white or colored, ranging from the lightest pink to the darkest purple tones according to the amount of anthocyanin accumulated in the berry skin, which is a crucial trait for both wine quality and human nutrition. Although the determinism of the white phenotype has been fully identified, the genetic bases of the quantitative variation of anthocyanin content in berry skin remain unclear. A single QTL responsible for up to 62% of the variation in the anthocyanin content was mapped on a Syrah × Grenache F1 pseudo-testcross. Among the 68 unigenes identified in the grape genome within the QTL interval, a cluster of four Myb-type genes was selected on the basis of physiological evidence (VvMybA1, VvMybA2, VvMybA3, and VvMybA4). From a core collection of natural resources (141 in iduals), 32 polymorphisms revealed significant association, and extended linkage disequilibrium was observed. Using a multivariate regression method, we demonstrated that five polymorphisms in VvMybA genes except VvMybA4 (one retrotransposon, three single nucleotide polymorphisms and one 2-bp insertion/deletion) accounted for 84% of the observed variation. All these polymorphisms led to either structural changes in the MYB proteins or differences in the VvMybAs promoters. We concluded that the continuous variation in anthocyanin content in grape was explained mainly by a single gene cluster of three VvMybA genes. The use of natural ersity helped to reduce one QTL to a set of five quantitative trait nucleotides and gave a clear picture of how isogenes combined their effects to shape grape color. Such analysis also illustrates how isogenes combine their effect to shape a complex quantitative trait and enables the definition of markers directly targeted for upcoming breeding programs.

Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana

Publisher: Proceedings of the National Academy of Sciences

Date: 02-05-2016

DOI: 10.1073/PNAS.1517456113

Abstract: Anticipating the effect of climate change on plants requires understanding its evolutionary consequence on traits and genes in complex realistic environments. How seasonal variation has an impact on the dynamics of adaptation in natural populations remains unclear. We simulated adaptation to different climate change scenarios, grounding our analysis in experimental data and explicitly exploring seasonal variation. Seasonal variation dramatically affected the dynamics of adaptation: Marked seasonality led to genetic differentiation within the population to different seasonal periods, whereas low seasonality led to a single population with fast-evolving fitness. Our results suggest the prevalence of phenotypic plasticity across environmental conditions in determining how climate change will shift selection on traits and loci. In this unpredictable context, maintaining broad genomic ersity is critical.

Loss of Neogenin1 in human colorectal carcinoma cells causes a partial EMT and wound-healing response

Publisher: Springer Science and Business Media LLC

Date: 11-03-2019

DOI: 10.1038/S41598-019-40886-Y

Abstract: Neogenin1 (NEO1) is a receptor of the Deleted in Colorectal Carcinoma (DCC)/Frazzled/UNC-40 family, which regulates axon guidance but can also stabilize epithelial adherens junctions. NEO1 and DCC are also tumor suppressors that can inhibit metastasis by acting as dependence receptors. Given the role of NEO1 in maintaining adherens junctions we tested whether loss of NEO1 also promoted metastasis via an epithelial mesenchymal transition (EMT). Loss of NEO1 disrupted zonula adherens but tight junctions were unaffected. Neo1- depleted epithelial cells exhibited a more migratory morphology, had reduced F-actin rich stress-fibres and more basal lamellipodia. Microtubule density was decreased while microtubule outgrowth was faster. Live imaging showed that Neo1 -depleted epithelial islands had increased lateral movement. Western blots and immunostaining revealed increased expression of mesenchymal markers such as Fibronectin and MMP1. Furthermore, RNA-seq analysis showed a striking decrease in expression of genes associated with oxidative phosphorylation, and increased expression of genes associated with EMT, locomotion, and wound-healing. In summary, loss of NEO1 in intestinal epithelial cells produces a partial EMT response, based on gene expression, cellular morphology and behaviour and cytoskeletal distribution. These results suggest that loss of NEO1 in carcinomas may contribute to metastasis by promoting a partial EMT and increased motility.

Multiple P450s and Variation in Neuronal Genes Underpins the Response to the Insecticide Imidacloprid in a Population of Drosophila melanogaster

Publisher: Springer Science and Business Media LLC

Date: 12-09-2017

DOI: 10.1038/S41598-017-11092-5

Abstract: Insecticide resistance is an economically important ex le of evolution in response to intense selection pressure. Here, the genetics of resistance to the neonicotinoid insecticide imidacloprid is explored using the Drosophila Genetic Reference Panel, a collection of inbred Drosophila melanogaster genotypes derived from a single population in North Carolina. Imidacloprid resistance varied substantially among genotypes, and more resistant genotypes tended to show increased capacity to metabolize and excrete imidacloprid. Variation in resistance level was then associated with genomic and transcriptomic variation, implicating several candidate genes involved in central nervous system function and the cytochrome P450s Cyp6g1 and Cyp6g2 . CRISPR-Cas9 mediated removal of Cyp6g1 suggested that it contributed to imidacloprid resistance only in backgrounds where it was already highly expressed. Cyp6g2 , previously implicated in juvenile hormone synthesis via expression in the ring gland, was shown to be expressed in metabolically relevant tissues of resistant genotypes. Cyp6g2 overexpression was shown to both metabolize imidacloprid and confer resistance. These data collectively suggest that imidacloprid resistance is influenced by a variety of previously known and unknown genetic factors.

Selection of candidate genes for grape proanthocyanidin pathway by an integrative approach

Publisher: Elsevier BV

Date: 11-2013

DOI: 10.1016/J.PLAPHY.2013.04.014

Abstract: Proanthocyanidins (PA) play a major role in plant protection against biotic and abiotic stresses. Moreover these molecules are known to be beneficial for human health and are responsible for astringency of foods and beverages such as wine and thus have a great impact on the final quality of the product. Genes playing a role in the PA pathway are only partially known. The amount of available transcriptomic and genetic data to select candidate genes without a priori knowledge from orthologous function increases every day. However, the methods used so far generate so many candidate genes that it is impossible to validate all of them. In this study, we used an integrative strategy based on different screening methods to select a reduced list of candidate genes. We have crossed results from different screening methods including QTL mapping and three transcriptomic studies to select 20 candidate genes, located in QTL intervals and fulfilling at least two transcriptomic screenings. This list includes three glucosyltransferases, already suspected to have a role in the PA biosynthetic pathway. Among the 17 remaining genes, we selected three genes to perform further analysis by association genetic studies. For each of these genes, we found a polymorphism linked to PA variation. The three genes (VvMybC2-L1, VvGAT-like and VvCob-like), not previously known to play a role in PA synthesis, are promising candidates for further molecular physiology studies.

Pollen competition in hybridizing Cakile species: How does a latecomer win the race?

Publisher: Wiley

Date: 08-2022

DOI: 10.1002/AJB2.16035

Abstract: Hybridization between cross‐compatible species depends on the extent of competition between alternative mates. Even if stigmatic compatibility allows for hybridization, hybridization requires the heterospecific pollen to be competitive. Here, we determined whether conspecific pollen has an advantage in the race to fertilize ovules and the potential handicap to be overcome by heterospecific pollen in invasive Cakile species. We used fluorescence microscopy to measure pollen tube growth after conspecific and heterospecific hand‐pollination treatments. We then determined siring success in the progeny relative to the timing of heterospecific pollen arrival on the stigma using CAPS markers. In the absence of pollen competition, pollination time and pollen recipient species had a significant effect on the ratio of pollen tube growth. In long‐styled C. maritima (outcrosser), pollen tubes grew similarly in both directions. In short‐styled C. edentula (selfer), conspecific and heterospecific pollen tubes grew differently. Cakile edentula pollen produced more pollen tubes, revealing the potential for a mating asymmetry whereby C. edentula pollen had an advantage relative to C. maritima . In the presence of pollen competition, siring success was equivalent when pollen deposition was synchronous. However, a moderate 1‐h advantage in the timing of conspecific pollination resulted in almost complete assortative mating, while an equivalent delay in conspecific pollination resulted in substantial hybrid formation. Hybridization can aid the establishment of invasive species through the transfer of adaptive alleles from cross‐compatible species, but also lead to extinction through demographic or genetic sw ing. Time of pollen arrival on the stigma substantially affected hybridization rate, pointing to the importance of pollination timing in driving introgression and genetic sw ing.

Structural Variants and Selective Sweep Foci Contribute to Insecticide Resistance in theDrosophilaGenetic Reference Panel

Publisher: Oxford University Press (OUP)

Date: 11-2018

DOI: 10.1534/G3.118.200619

Abstract: Patterns 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 sweeps 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, 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 allele 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.

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

Publisher: Proceedings of the National Academy of Sciences

Date: 07-05-2019

DOI: 10.1073/PNAS.1821713116

Abstract: Around 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 coregulated detoxification genes. We predict that these variants will increase in populations of this “sentinel species” as these insecticides are applied in the environment.

The International Weed Genomics Consortium: Community Resources for Weed Genomics Research

Publisher: Cold Spring Harbor Laboratory

Date: 20-07-2023

DOI: 10.1101/2023.07.19.549613

Abstract: The International Weed Genomics Consortium is a collaborative group of researchers focused on developing genomic resources for the study of weedy plants. Weeds are attractive systems for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Our goal is to use genomic information to develop sustainable and effective weed control methods and to provide insights about biotic and abiotic stress tolerance to assist crop breeding. Here, we outline resources under development by the consortium and highlight areas of research that will be impacted by these enabling resources.

The spread of resistance to imidacloprid is restricted by thermotolerance in natural populations of Drosophila melanogaster

Publisher: Springer Science and Business Media LLC

Date: 18-03-2019

DOI: 10.1038/S41559-019-0837-Y

Abstract: Imidacloprid, the world's most used insecticide, has caused considerable controversy due to harmful effects on non-pest species and increasing evidence showing that insecticides have become the primary selective force in many insect species. The genetic response to insecticides is heterogeneous across populations and environments, leading to more complex patterns of genetic variation than previously thought. This motivated the investigation of imidacloprid resistance at different temperatures in natural populations of Drosophila melanogaster originating from four climate extremes replicated across two continents. Population and quantitative genomic analysis, supported by functional tests, have revealed a mixed genetic architecture to resistance involving major genes (Paramyosin and Nicotinic-Acetylcholine Receptor Alpha 3) and polygenes with a major trade-off with thermotolerance. Reduced genetic differentiation at resistance-associated loci indicated enhanced gene flow at these loci. Resistance alleles showed stronger evidence of positive selection in temperate populations compared to tropical populations in which chromosomal inversions In(2 L)t, In(3 R)Mo and In(3 R)Payne harbour susceptibility alleles. Polygenic architecture and ecological factors should be considered when developing sustainable management strategies for both pest and beneficial insects.

Behavioural response to combined insecticide and temperature stress in natural populations of Drosophila melanogaster

Publisher: Wiley

Date: 17-03-2016

DOI: 10.1111/JEB.12844

Abstract: Insecticide resistance evolves extremely rapidly, providing an illuminating model for the study of adaptation. With climate change reshaping species distribution, pest and disease vector control needs rethinking to include the effects of environmental variation and insect stress physiology. Here, we assessed how both long-term adaptation of populations to temperature and immediate temperature variation affect the genetic architecture of DDT insecticide response in Drosophila melanogaster. Mortality assays and behavioural assays based on continuous activity monitoring were used to assess the interaction between DDT and temperature on three field-derived populations from climate extremes (Raleigh for warm temperate, Tasmania for cold oceanic and Queensland for hot tropical). The Raleigh population showed the highest mortality to DDT, whereas the Queensland population, epicentre for derived alleles of the resistance gene Cyp6g1, showed the lowest. Interaction between insecticide and temperature strongly affected mortality, particularly for the Tasmanian population. Activity profiles analysed using self-organizing maps show that the insecticide promoted an early response, whereas elevated temperature promoted a later response. These distinctive early or later activity phases revealed similar responses to temperature and DDT dose alone but with more or less genetic variance depending on the population. This change in genetic variance among populations suggests that selection particularly depleted genetic variance for DDT response in the Queensland population. Finally, despite similar (co)variation between traits in benign conditions, the genetic responses across population differed under stressful conditions. This showed how stress-responsive genetic variation only reveals itself in specific conditions and thereby escapes potential trade-offs in benign environments.

A Map of Local Adaptation in Arabidopsis thaliana

Publisher: American Association for the Advancement of Science (AAAS)

Date: 07-10-2011

DOI: 10.1126/SCIENCE.1209271

Abstract: Field experiments identify loci associated with fitness and local adaptation in Arabidopsis.

Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp sativa

Publisher: Springer Science and Business Media LLC

Date: 2008

DOI: 10.1186/1471-2229-8-31

The Wiggle Index: An Open Source Bioassay to Assess Sub-Lethal Insecticide Response in Drosophila melanogaster

Publisher: Public Library of Science (PLoS)

Date: 18-12-2015

DOI: 10.1371/JOURNAL.PONE.0145051

Paths to selection on life history loci in different natural environments across the native range of Arabidopsis thaliana

Publisher: Wiley

Date: 18-03-2013

DOI: 10.1111/MEC.12285

Abstract: Selection on quantitative trait loci (QTL) may vary among natural environments due to differences in the genetic architecture of traits, environment-specific allelic effects or changes in the direction and magnitude of selection on specific traits. To dissect the environmental differences in selection on life history QTL across climatic regions, we grew a panel of interconnected recombinant inbred lines (RILs) of Arabidopsis thaliana in four field sites across its native European range. For each environment, we mapped QTL for growth, reproductive timing and development. Several QTL were pleiotropic across environments, three colocalizing with known functional polymorphisms in flowering time genes (CRY2, FRI and MAF2-5), but major QTL differed across field sites, showing conditional neutrality. We used structural equation models to trace selection paths from QTL to lifetime fitness in each environment. Only three QTL directly affected fruit number, measuring fitness. Most QTL had an indirect effect on fitness through their effect on bolting time or leaf length. Influence of life history traits on fitness differed dramatically across sites, resulting in different patterns of selection on reproductive timing and underlying QTL. In two oceanic field sites with high prereproductive mortality, QTL alleles contributing to early reproduction resulted in greater fruit production, conferring selective advantage, whereas alleles contributing to later reproduction resulted in larger size and higher fitness in a continental site. This demonstrates how environmental variation leads to change in both QTL effect sizes and direction of selection on traits, justifying the persistence of allelic polymorphism at life history QTL across the species range.

GWAlpha: Genome-wide estimation of additive effects (alpha) based on trait quantile distribution from pool-sequencing experiments

Publisher: Oxford University Press (OUP)

Date: 21-12-2017

DOI: 10.1093/BIOINFORMATICS/BTW805

Abstract: Sequencing pools of in iduals (Pool-Seq) is a cost-effective way to gain insight into the genetics of complex traits, but as yet no parametric method has been developed to both test for genetic effects and estimate their magnitude. Here, we propose GWAlpha, a flexible method to obtain parametric estimates of genetic effects genome-wide from Pool-Seq experiments. We showed that GWAlpha powerfully replicates the results of Genome-Wide Association Studies (GWAS) from model organisms. We perform simulation studies that illustrate the effect on power of s le size and number of pools and test the method on different experimental data. GWAlpha is implemented in python, designed to run on Linux operating system and tested on Mac OS. It is freely available at flevel/GWAlpha. Supplementary data are available at Bioinformatics online.

Genetic mechanisms underlying the methylation level of anthocyanins in grape (Vitis viniferaL.)

Publisher: Springer Science and Business Media LLC

Date: 12-2011

DOI: 10.1186/1471-2229-11-179

Abstract: Plant color variation is due not only to the global pigment concentration but also to the proportion of different types of pigment. Variation in the color spectrum may arise from secondary modifications, such as hydroxylation and methylation, affecting the chromatic properties of pigments. In grapes ( Vitis vinifera L.), the level of methylation modifies the stability and reactivity of anthocyanin, which directly influence the color of the berry. Anthocyanin methylation, as a complex trait, is controlled by multiple molecular factors likely to involve multiple regulatory steps. In a Syrah × Grenache progeny, two QTLs were detected for variation in level of anthocyanin methylation. The first one, explaining up to 27% of variance, colocalized with a cluster of Myb-type transcription factor genes. The second one, explaining up to 20% of variance, colocalized with a cluster of O- methyltransferase coding genes (AOMT). In a collection of 32 unrelated cultivars, MybA and AOMT expression profiles correlated with the level of methylated anthocyanin. In addition, the newly characterized AOMT2 gene presented two SNPs associated with methylation level. These mutations, probably leading to a structural change of the AOMT2 protein significantly affected the enzyme specific catalytic efficiency for the 3'- O- methylation of delphinidin 3-glucoside. We demonstrated that variation in methylated anthocyanin accumulation is susceptible to involve both transcriptional regulation and structural variation. We report here the identification of novel AOMT variants likely to cause methylated anthocyanin variation. The integration of QTL mapping and molecular approaches enabled a better understanding of how variation in gene expression and catalytic efficiency of the resulting enzyme may influence the grape anthocyanin profile.

Rounding up the annual ryegrass genome: high-quality reference genome of Lolium rigidum

Publisher: Cold Spring Harbor Laboratory

Date: 19-07-2022

DOI: 10.1101/2022.07.18.499821

Abstract: The genome of the major agricultural weed species, annual ryegrass ( Lolium rigidum ) was assembled, annotated and analysed. Annual ryegrass is a major weed in wheat cropping, and has the remarkable capacity to evolve resistance to herbicides with various modes of action. The chromosome-level assembly was achieved using short- and long-read sequencing in combination with Hi-C mapping. The assembly size is 2.44Gb with N 50 =361.79Mb across 1,764 scaffolds where the seven longest sequences correspond to the seven chromosomes. Genome completeness assessed through BUSCO returned a 99.8% score for complete (unique and duplicated) and fragmented genes using the Viridiplantae set. We found evidence for the expansion of herbicide resistance-related gene families including detoxification genes. The reference genome assembly of L. rigidum is pivotal for the management of this highly problematic weed species which leverages genomic tools to devise new control options.

What can genetic association panels tell us about evolutionary processes in insects?

Publisher: Elsevier BV

Date: 02-2019

DOI: 10.1016/J.COIS.2018.12.004

Abstract: If we are to fully comprehend the evolution of insect ersity at a genomic level we need to understand how natural selection can alter genetically encoded characters within populations. Genetic association panels have the potential to be standard bearers in this endeavour. They enable the mapping of phenotypes to genotypes at unprecedented resolution while simultaneously providing population genomic s les that can be interrogated for the tell-tale signs of selection. Analyses of these panels promise to elucidate the entanglement of gene ontologies, pathways, developmental processes and evolutionary constraints, and inform how these are shaped by adaptation.

Genomic and Transcriptomic Associations Identify a New Insecticide Resistance Phenotype for the Selective Sweep at the Cyp6g1 Locus of Drosophila melanogaster

Publisher: Oxford University Press (OUP)

Date: 08-2016

DOI: 10.1534/G3.116.031054

Abstract: Scans of the Drosophila melanogaster genome have identified organophosphate resistance loci among those with the most pronounced signature of positive selection. In this study, the molecular basis of resistance to the organophosphate insecticide azinphos-methyl was investigated using the Drosophila Genetic Reference Panel, and genome-wide association. Recently released full transcriptome data were used to extend the utility of the Drosophila Genetic Reference Panel resource beyond traditional genome-wide association studies to allow systems genetics analyses of phenotypes. We found that both genomic and transcriptomic associations independently identified Cyp6g1, a gene involved in resistance to DDT and neonicotinoid insecticides, as the top candidate for azinphos-methyl resistance. This was verified by transgenically overexpressing Cyp6g1 using natural regulatory elements from a resistant allele, resulting in a 6.5-fold increase in resistance. We also identified four novel candidate genes associated with azinphos-methyl resistance, all of which are involved in either regulation of fat storage, or nervous system development. In Cyp6g1, we find a demonstrable resistance locus, a verification that transcriptome data can be used to identify variants associated with insecticide resistance, and an overlap between peaks of a genome-wide association study, and a genome-wide selective sweep analysis.

Adaptive significance of flowering time variation across natural seasonal environments in Arabidopsis thaliana.

Publisher: Wiley

Date: 23-02-2022

DOI: 10.1111/NPH.17999

Abstract: The relevance of flowering time variation and plasticity to climate adaptation requires a comprehensive empirical assessment. We investigated natural selection and the genetic architecture of flowering time in Arabidopsis through field experiments in Europe across multiple sites and seasons. We estimated selection for flowering time, plasticity and canalization. Loci associated with flowering time, plasticity and canalization by genome-wide association studies were tested for a geographic signature of climate adaptation. Selection favored early flowering and increased canalization, except at the northernmost site, but was rarely detected for plasticity. Genome-wide association studies revealed significant associations with flowering traits and supported a substantial polygenic inheritance. Alleles associated with late flowering, including functional FRIGIDA variants, were more common in regions experiencing high annual temperature variation. Flowering time plasticity to fall vs spring and summer environments was associated with GIGANTEA SUPPRESSOR 5, which promotes early flowering under decreasing day length and temperature. The finding that late flowering genotypes and alleles are associated with climate is evidence for past adaptation. Real-time phenotypic selection analysis, however, reveals pervasive contemporary selection for rapid flowering in agricultural settings across most of the species range. The response to this selection may involve genetic shifts in environmental cuing compared to the ancestral state.

Structural variants and selective sweep foci contribute to insecticide resistance in theDrosophila melanogastergenetic reference panel

Publisher: Cold Spring Harbor Laboratory

Date: 16-04-2018

DOI: 10.1101/301937

Abstract: Patterns 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.

Comparative Genomics Points to Tandem Duplications ofSADGene Clusters as Drivers of Increased ω-3 Content inS. hispanicaSeeds

Publisher: Cold Spring Harbor Laboratory

Date: 28-08-2023

DOI: 10.1101/2023.08.27.555029

Abstract: A high-quality chromosome-level reference genome of S. hispanica was assembled and analysed. Ancestral whole-genome duplication events have not promoted the high α-linolenic acid content in S. hispanica seeds Tandem duplication of six stearoyl-ACP desaturase genes is a plausible cause for high ω-3 content in chia seeds. Salvia hispanica L. (chia) is an abundant source of ω-3 polyunsaturated fatty acids (PUFAs) that are highly beneficial to human health. The genomic basis for this accrued PUFA content in this emerging crop was investigated through the assembly and comparative analysis of a chromosome-level reference genome for S. hispanica (321.5 Mbp). The highly contiguous 321.5Mbp genome assembly, which covers all six chromosomes enabled the identification of 32,922 protein coding genes. Two whole-genome duplications (WGD) events were identified in the S. hispanica lineage. However, these WGD events could not be linked to the high α-linolenic acid (ALA, ω-3) accumulation in S. hispanica seeds based on phylogenomics. Instead, our analysis supports the hypothesis that evolutionary expansion through tandem duplications of specific lipid gene families, particularly the stearoyl-acyl carrier protein (ACP) desaturase ( ShSAD ) gene family, is the main driver of the abundance of ω-3 PUFAs in S. hispanica seeds. The insights gained from the genomic analysis of S. hispanica will help leveraging advanced genome editing techniques and will greatly support breeding efforts for improving ω-3 content in other oil crops.

instaGraminoid, a Novel Colorimetric Method to Assess Herbicide Resistance, Identifies Patterns of Cross-Resistance in Annual Ryegrass

Publisher: American Association for the Advancement of Science (AAAS)

Date: 2019

DOI: 10.34133/2019/7937156

Abstract: Herbicide resistance in agricultural weeds is a global problem with an increasing understanding that it is caused by multiple genes leading to quantitative resistance. These quantitative patterns of resistance are not easy to decipher with mortality assays alone, and there is a need for straightforward and unbiased protocols to accurately assess quantitative herbicide resistance. instaGraminoid —a computer vision and statistical analysis package—was developed as an automated and scalable method for quantifying herbicide resistance. The package was tested in rigid ryegrass ( Lolium rigidum ), the most noxious and highly resistant weed in Australia and the Mediterranean region. This method provides quantitative measures of the degree of chlorosis and necrosis of in idual plants which was shown to accurately reflect herbicide resistance. We were able to reliably characterise resistance to four herbicides with different sites of action (glyphosate, sulfometuron, terbuthylazine, and trifluralin) in two L. rigidum populations from Southeast Australia. Cross-validation of the method across populations and herbicide treatments showed high repeatability and transferability. Significant positive correlations in resistance of in idual plants were observed across herbicides, which suggest either the accumulation of herbicide-specific resistance alleles in single genotypes (multiple stacked resistance) or the presence of general broad-effects resistance alleles (cross-resistance). We used these quantitative estimates of cross-resistance to simulate how resistance development under an herbicide rotation strategy is likely to be higher than expected.

Insights into DDT Resistance from the Drosophila melanogaster Genetic Reference Panel

Publisher: Oxford University Press (OUP)

Date: 21-09-2017

DOI: 10.1534/GENETICS.117.300310

Abstract: Insecticide resistance is considered a classic model of microevolution, where a strong selective agent is applied to a large natural population, resulting in a change in frequency of alleles that confer resistance. While many insecticide resistance variants have been characterized at the gene level, they are typically single genes of large effect identified in highly resistant pest species. In contrast, multiple variants have been implicated in DDT resistance in Drosophila melanogaster however, only the Cyp6g1 locus has previously been shown to be relevant to field populations. Here we use genome-wide association studies (GWAS) to identify DDT-associated polygenes and use selective sweep analyses to assess their adaptive significance. We identify and verify two candidate DDT resistance loci. A largely uncharacterized gene, CG10737, has a function in muscles that ameliorates the effects of DDT, while a putative detoxifying P450, Cyp6w1, shows compelling evidence of positive selection.

Modelling the effect of migration on the localisation and spread of a gene drive

Publisher: Cold Spring Harbor Laboratory

Date: 04-04-2023

DOI: 10.1101/2023.04.02.535303

Abstract: Gene drives have the potential to address pressing ecological issues. Through the super-Mendelian inheritance of a gene drive, a trait can be spread through a population even in spite of a fitness cost. This ability to spread is both its greatest quality and detractor. We may not want a gene drive to spread universally. If a gene drive were designed to cause the collapse of a pest population, it may inadvertently cause the collapse of the entire species. Migration is the mechanism through which a gene drive can spread to distant populations. Understanding its effect on the progression of a gene drive is crucial to our ability to control a gene drive. While migration can spread the gene drive to other populations, equally it can bring in other alleles to the population that may disrupt the progression of the gene drive. Through our deterministic migration gene drive model we can assess the conditions in which a gene drive is likely to spread to unintended populations, and if a gene drive is likely to be displaced by incoming alleles.

Forecasting trait responses in novel environments to aid seed provenancing under climate change

Publisher: Wiley

Date: 10-11-2022

DOI: 10.1111/1755-0998.13728

Abstract: Revegetation projects face the major challenge of sourcing optimal plant material. This is often done with limited information about plant performance and increasingly requires factoring resilience to climate change. Functional traits can be used as quantitative indices of plant performance and guide seed provenancing, but trait values expected under novel conditions are often unknown. To support climate‐resilient provenancing efforts, we develop a trait prediction model that integrates the effect of genetic variation with fine‐scale temperature variation. We train our model on multiple field plantings of Arabidopsis thaliana and predict two relevant fitness traits—days‐to‐bolting and fecundity—across the species' European range. Prediction accuracy was high for days‐to‐bolting and moderate for fecundity, with the majority of trait variation explained by temperature differences between plantings. Projection under future climate predicted a decline in fecundity, although this response was heterogeneous across the range. In response, we identified novel genotypes that could be introduced to genetically offset the fitness decay. Our study highlights the value of predictive models to aid seed provenancing and improve the success of revegetation projects.

Sublethal larval exposure to imidacloprid impacts adult behaviour in Drosophila melanogaster

Publisher: Wiley

Date: 19-11-2019

DOI: 10.1111/JEB.13555

Abstract: Pesticides are now chronically found in numerous ecosystems incurring widespread toxic effects on multiple organisms. For insects, the larvae are very exposed to pesticide pollution and the acute effect of insecticides on larvae has been characterized in a range of species. However, the carry-on effects in adults of sublethal exposure occurring in larvae are not well characterized. Here, we use a collection of strains of Drosophila melanogaster differing in their larval resistance to a commonly used insecticide, imidacloprid, and we test the effect of larval exposure on behavioural traits at the adult stage. Focusing on locomotor activity and on courtship and mating behaviour, we observed a significant carry-on effect of imidacloprid exposure. The heritability of activity traits measured in flies exposed to imidacloprid was higher than measured in controls and in these, courtship traits were genetically less correlated from mating success. Altogether, we did not observe a significant effect of the larval insecticide resistance status on adult behavioural traits, suggesting that selection for resistance in larvae does not involve repeatable behavioural changes in adults. This lack of correlation between larval resistance and adult behaviour also suggests that resistance at the larval stage does not necessarily result in increased behavioural resilience at a later life stage. These findings imply that selection for resistance in larvae as well as for behavioural resilience to sublethal exposure in adult will combine and impose a greater evolutionary constraint. Our conclusions further substantiate the need to encompass multiple trait measures and life stages in toxicological assays to properly assess the environmental impact of pesticides.

University Of Melbourne

Location: Australia

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Université De Montpellier

Location: France

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The Transgenerational Effect Of Thermosensing In Plants

Start Date: 2019

End Date: 2022

Funder: Australian Research Council

Discovery Projects - Grant ID: DP190101818

Start Date: 04-2019

End Date: 09-2024

Amount: $487,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP220102362

Start Date: 08-2022

End Date: 08-2025

Amount: $486,315.00

Funder: Australian Research Council