scholarly journals Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

2021 ◽  
Author(s):  
Sonja Kersten ◽  
Jiyang Chang ◽  
Christian D Huber ◽  
Yoav Voichek ◽  
Christa Lanz ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Herbicide Resistance ◽  
Large Scale ◽  
De Novo ◽  
Bulked Segregant Analysis ◽  
Target Site ◽  
Temperate Climate ◽  
Minor Role ◽  
Standing Variation ◽  
Target Site Resistance

Repeated herbicide applications exert enormous selection on blackgrass (Alopecurus myosuroides), a major weed in cereal crops of the temperate climate zone including Europe. This inadvertent large-scale experiment gives us the opportunity to look into the underlying genetic mechanisms and evolutionary processes of rapid adaptation, which can occur both through mutations in the direct targets of herbicides and through changes in other, often metabolic, pathways, known as non-target-site resistance. How much either type of adaptation relies on de novo mutations versus pre-existing standing variation is important for developing strategies to manage herbicide resistance. We generated a chromosome-level reference genome for A. myosuroides for population genomic studies of herbicide resistance and genome-wide diversity across Europe in this species. Bulked-segregant analysis evidenced that non-target-site resistance has a complex genetic architecture. Through empirical data and simulations, we showed that, despite its simple genetics, target-site resistance mainly results from standing genetic variation, with only a minor role for de novo mutations.

scholarly journals The genetic architecture and genomic context of glyphosate resistance

2020 ◽  
Author(s):  
J.M. Kreiner ◽  
P.J. Tranel ◽  
D. Weigel ◽  
J.R. Stinchcombe ◽  
S.I. Wright
Keyword(s):  
Herbicide Resistance ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Glyphosate Resistance ◽  
Target Site ◽  
Plant Performance ◽  
Comparable Amount ◽  
Standing Variation ◽  
Genome Wide ◽  
Target Site Resistance

AbstractAlthough much of what we know about the genetic basis of herbicide resistance has come from detailed investigations of monogenic adaptation at known target-sites, the importance of polygenic resistance has been increasingly recognized. Despite this, little work has been done to characterize the genomic basis of herbicide resistance, including the number and distribution of involved genes, their effect sizes, allele frequencies, and signatures of selection. Here we implement genome-wide association (GWA) and population genomic approaches to examine the genetic architecture of glyphosate resistance in the problematic agricultural weed, Amaranthus tuberculatus. GWA correctly identifies the gene targeted by glyphosate, and additionally finds more than 100 genes across all 16 chromosomes associated with resistance. The encoded proteins have relevant non-target-site resistance and stress-related functions, with potential for pleiotropic roles in resistance to other herbicides and diverse life history traits. Resistance-related alleles are enriched for large effects and intermediate frequencies, implying that strong selection has shaped the genetic architecture of resistance despite potential pleiotropic costs. The range of common and rare allele involvement implies a partially shared genetic basis of non-target-site resistance across populations, complemented by population-specific alleles. Resistance-related alleles show evidence of balancing selection, and suggest a long-term maintenance of standing variation at stress-response loci that have implications for plant performance under herbicide pressure. By our estimates, genome-wide SNPs explain a comparable amount of the total variation in glyphosate resistance to monogenic mechanisms, indicating the potential for an underappreciated polygenic contribution to the evolution of herbicide resistance in weed populations.

scholarly journals Molecular Mechanisms of Herbicide Resistance

Weed Science ◽  
2015 ◽  
Vol 63 (SP1) ◽  
pp. 91-115 ◽  
Author(s):  
Christophe Délye ◽  
Arnaud Duhoux ◽  
Fanny Pernin ◽  
Chance W. Riggins ◽  
Patrick J. Tranel
Keyword(s):  
Herbicide Resistance ◽  
Molecular Mechanisms ◽  
Target Site ◽  
Target Protein ◽  
Intrinsic Activity ◽  
Evolutionary Adaptation ◽  
Herbicide Binding ◽  
Target Site Resistance ◽  
Resistance To Herbicides ◽  
Increased Activity

Resistance to herbicides occurs in weeds as the result of evolutionary adaptation (Jasieniuk et al. 1996). Basically, two types of mechanisms are involved in resistance (Beckie and Tardif 2012; Délye 2013). Target-site resistance (TSR) is caused by changes in the tridimensional structure of the herbicide target protein that decrease herbicide binding, or by increased activity (e.g., due to increased expression or increased intrinsic activity) of the target protein. Nontarget-site resistance (NTSR) is endowed by any mechanism not belonging to TSR, e.g., reduction in herbicide uptake or translocation in the plant, or enhanced herbicide detoxification (reviewed in Délye 2013; Yuan et al. 2007).

scholarly journals Rapid low-cost assembly of the Drosophila melanogaster reference genome using low-coverage, long-read sequencing

2018 ◽  
Author(s):  
Edwin A. Solares ◽  
Mahul Chakraborty ◽  
Danny E. Miller ◽  
Shannon Kalsow ◽  
Kate Hall ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Large Scale ◽  
Reference Genome ◽  
De Novo ◽  
Low Cost ◽  
Nucleotide Polymorphisms ◽  
Structural Variants ◽  
High Coverage ◽  
Reference Assembly

ABSTRACTAccurate and comprehensive characterization of genetic variation is essential for deciphering the genetic basis of diseases and other phenotypes. A vast amount of genetic variation stems from large-scale sequence changes arising from the duplication, deletion, inversion, and translocation of sequences. In the past 10 years, high-throughput short reads have greatly expanded our ability to assay sequence variation due to single nucleotide polymorphisms. However, a recent de novo assembly of a second Drosophila melanogaster reference genome has revealed that short read genotyping methods miss hundreds of structural variants, including those affecting phenotypes. While genomes assembled using high-coverage long reads can achieve high levels of contiguity and completeness, concerns about cost, errors, and low yield have limited widespread adoption of such sequencing approaches. Here we resequenced the reference strain of D. melanogaster (ISO1) on a single Oxford Nanopore MinION flow cell run for 24 hours. Using only reads longer than 1 kb or with at least 30x coverage, we assembled a highly contiguous de novo genome. The addition of inexpensive paired reads and subsequent scaffolding using an optical map technology achieved an assembly with completeness and contiguity comparable to the D. melanogaster reference assembly. Comparison of our assembly to the reference assembly of ISO1 uncovered a number of structural variants (SVs), including novel LTR transposable element insertions and duplications affecting genes with developmental, behavioral, and metabolic functions. Collectively, these SVs provide a snapshot of the dynamics of genome evolution. Furthermore, our assembly and comparison to the D. melanogaster reference genome demonstrates that high-quality de novo assembly of reference genomes and comprehensive variant discovery using such assemblies are now possible by a single lab for under $1,000 (USD).

scholarly journals How does adaptation sweep through the genome? Insights from long-term selection experiments

2012 ◽  
Vol 279 (1749) ◽  
pp. 5029-5038 ◽  
Author(s):  
Molly K. Burke
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Population Biology ◽  
De Novo ◽  
Whole Genome ◽  
Beneficial Mutations ◽  
Adaptive Mutations ◽  
Laboratory Selection ◽  
Standing Variation ◽  
New Mutations

A major goal in evolutionary biology is to understand the origins and fates of adaptive mutations. Natural selection may act to increase the frequency of de novo beneficial mutations, or those already present in the population as standing genetic variation. These beneficial mutations may ultimately reach fixation in a population, or they may stop increasing in frequency once a particular phenotypic state has been achieved. It is not yet well understood how different features of population biology, and/or different environmental circumstances affect these adaptive processes. Experimental evolution is a promising technique for studying the dynamics of beneficial alleles, as populations evolving in the laboratory experience natural selection in a replicated, controlled manner. Whole-genome sequencing, regularly obtained over the course of sustained laboratory selection, could potentially reveal insights into the mutational dynamics that most likely occur in natural populations under similar circumstances. To date, only a few evolution experiments for which whole-genome data are available exist. This review describes results from these resequenced laboratory-selected populations, in systems with and without sexual recombination. In asexual systems, adaptation from new mutations can be studied, and results to date suggest that the complete, unimpeded fixation of these mutations is not always observed. In sexual systems, adaptation from standing genetic variation can be studied, and in the admittedly few examples we have, the complete fixation of standing variants is not always observed. To date, the relative frequency of adaptation from new mutations versus standing variation has not been tested using a single experimental system, but recent studies using Caenorhabditis elegans and Saccharomyces cerevisiae suggest that this a realistic future goal.

scholarly journals Herbicide Resistance and Management Options of Papaver rhoeas L. and Centaurea cyanus L. in Europe: A Review

Agronomy ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 874
Author(s):  
Marta Stankiewicz-Kosyl ◽  
Agnieszka Synowiec ◽  
Małgorzata Haliniarz ◽  
Anna Wenda-Piesik ◽  
Krzysztof Domaradzki ◽  
...  
Keyword(s):  
Herbicide Resistance ◽  
Acetolactate Synthase ◽  
Agricultural Landscapes ◽  
Target Site ◽  
Management Options ◽  
Papaver Rhoeas ◽  
Herbicide Resistant ◽  
Mediterranean Countries ◽  
Centaurea Cyanus ◽  
Target Site Resistance

Corn poppy (Papaver rhoeas L.) and cornflower (Centaurea cyanus L.) are two overwintering weed species found in crop fields in Europe. They are characterised by a similar life cycle, similar competitive efforts, and a spectrum of herbicides recommended for their control. This review summarises the biology and herbicide resistance phenomena of corn poppy and cornflower in Europe. Corn poppy is one of the most dangerous dicotyledonous weeds, having developed herbicide resistance to acetolactate synthase inhibitors and growth regulators, especially in Mediterranean countries and Great Britain. Target site resistance to acetolactate synthase inhibitors dominates among herbicide-resistant poppy biotypes. The importance of non-target site resistance to acetolactate synthase inhibitors in this species may be underestimated because non-target site resistance is very often associated with target site resistance. Cornflower, meanwhile, is increasingly rare in European agricultural landscapes, with acetolactate synthase inhibitors-resistant biotypes only listed in Poland. However, the mechanisms of cornflower herbicide resistance are not well recognised. Currently, herbicides mainly from acetolactate synthase and photosystem II inhibitors as well as from synthetic auxins groups are recommended for the control of both weeds. Integrated methods of management of both weeds, especially herbicide-resistant biotypes, continue to be underrepresented.

scholarly journals First evidence of multiple resistance of Sumatran Fleabane (Conyza sumatrensis (Retz.) E.Walker) to five- mode-of-action herbicides

2019 ◽  
pp. 1688-1697 ◽  
Author(s):  
Camila Ferreira de Pinho ◽  
Jessica Ferreira Lourenço Leal ◽  
Amanda dos Santos Souza ◽  
Gabriella Francisco Pereira Borges de Oliveira ◽  
Claudia de Oliveira ◽  
...  
Keyword(s):  
Herbicide Resistance ◽  
Mode Of Action ◽  
Resistance Index ◽  
Target Site ◽  
Multiple Resistance ◽  
First Case ◽  
Evolutionary Response ◽  
Target Site Resistance ◽  
Index Ratio ◽  
Dose Responses

Herbicide resistance is the evolutionary response of weeds to the selection pressure caused by repeated application of the same active ingredient. It can result from two different mechanisms, known as target site resistance (TSR) and non-target site resistance (NTSR). In addition to single-herbicide resistance, multiple resistance can occur due to herbicides selection or accumulation of resistance genes by cross-pollination. The aim of this research was to investigate the suspect of multiple herbicide resistance of Sumatran Fleabane (Conyza sumatrensis (Retz.) E.Walker) to herbicides frequently used as a burndown application. Dose-responses in a whole-plant assay were carried out to investigate multiple-resistance of Sumatran fleabane to paraquat, saflufenacil, diuron, 2,4-D and glyphosate. Results indicated that the resistance index (ratio R/S) based on herbicide rate to cause 50% mortality (LD50) were 25.51, 1.39, 7.29, 1.84 and 7.55 for paraquat, saflufenacil, diuron, 2,4-D and glyphosate, respectively. Based on herbicide rate required to cause a 50% reduction in plant growth (GR50), the resistant index were 51.83, 14.10, 5.05, 3.96 and 32.90 for the same herbicides, respectively. Our results confirmed multiple resistance of Conyza sumatrensis from Paraná-Brazil to herbicides from five-mode of-action. This was the first report of Conyza sumatrensis resistant to 2,4-D and the first case of Conyza sumatrensis presenting multiple resistant to herbicides from five- mode of-action in the world.

scholarly journals Weed resistance to herbicides

2020 ◽  
Vol 29 (2) ◽  
pp. 79-96
Author(s):  
Sava Vrbničanin
Keyword(s):  
Herbicide Resistance ◽  
Amaranthus Retroflexus ◽  
Ambrosia Artemisiifolia ◽  
Target Site ◽  
Weed Species ◽  
Ps Ii ◽  
Target Site Resistance ◽  
Resistance To Herbicides ◽  
Als Inhibitors ◽  
Weed Resistance

Weed resistance to herbicides represents the acquired resistance of individuals to complete the life cycle and leave offspring in the conditions of extended exposure to the same herbicide, i.e. herbicides of the same mechanism of action to which they were sensitive at the beginning of the application. Based on the herbicide resistance mechanisms, all processes can be grouped as follows: target-site resistance, non-target-site resistance, cross-resistance and multiple-resistance. Currently, herbicide resistance has been reported in 514 cases (species x site of action) worldwide, in 262 weed species (152 dicotyledons, 110 monocotyledons). Many of those biotypes are resistant to als inhibitors, PS II inhibitors, EPSPS inhibitors and ACC-ase inhibitors. The higher degree of resistance to als inhibitors has been confirmed in the following weed species: Amaranthus retroflexus, Sorghum halepense, Ambrosia artemisiifolia and Helianthus annuus.

scholarly journals Catch me if you can: Adaptation from standing genetic variation to a moving phenotypic optimum

2015 ◽  
Author(s):  
Sebastian Matuszewski ◽  
Joachim Hermisson ◽  
Michael Kopp
Keyword(s):  
Genetic Variation ◽  
De Novo ◽  
Darwinian Evolution ◽  
De Novo Mutations ◽  
Population Means ◽  
Standing Variation ◽  
Analytical Approximations ◽  
Formal Framework ◽  
Phenotype Space ◽  
Effect Size Distribution

Adaptation lies at the heart of Darwinian evolution. Accordingly, numerous studies have tried to provide a formal framework for the description of the adaptive process. Out of these, two complementary modelling approaches have emerged: While so-called adaptive-walk models consider adaptation from the successive fixation of de-novo mutations only, quantitative genetic models assume that adaptation proceeds exclusively from pre-existing standing genetic variation. The latter approach, however, has focused on short-term evolution of population means and variances rather than on the statistical properties of adaptive substitutions. Our aim is to combine these two approaches by describing the ecological and genetic factors that determine the genetic basis of adaptation from standing genetic variation in terms of the effect-size distribution of individual alleles. Specifically, we consider the evolution of a quantitative trait to a gradually changing environment. By means of analytical approximations, we derive the distribution of adaptive substitutions from standing genetic variation, that is, the distribution of the phenotypic effects of those alleles from the standing variation that become fixed during adaptation. Our results are checked against individual-based simulations. We find that, compared to adaptation from de-novo mutations, (i) adaptation from standing variation proceeds by the fixation of more alleles of small effect; (ii) populations that adapt from standing genetic variation can traverse larger distances in phenotype space and, thus, have a higher potential for adaptation if the rate of environmental change is fast rather than slow.

scholarly journals Herbicide-resistant weeds in turfgrass: current status and emerging threats

2020 ◽  
Vol 34 (3) ◽  
pp. 424-430
Author(s):  
James T. Brosnan ◽  
Matthew T. Elmore ◽  
Muthukumar V. Bagavathiannan
Keyword(s):  
United States ◽  
Herbicide Resistance ◽  
Production Systems ◽  
The United States ◽  
Target Site ◽  
Current Status ◽  
Weed Species ◽  
Management Tools ◽  
Herbicide Resistant ◽  
Target Site Resistance

AbstractHerbicide-resistant weeds pose a severe threat to sustainable vegetation management in various production systems worldwide. The majority of the herbicide resistance cases reported thus far originate from agronomic production systems where herbicide use is intensive, especially in industrialized countries. Another notable sector with heavy reliance on herbicides for weed control is managed turfgrass systems, particularly golf courses and athletic fields. Intensive use of herbicides, coupled with a lack of tillage and other mechanical tools that are options in agronomic systems, increases the risk of herbicide-resistant weeds evolving in managed turfgrass systems. Among the notable weed species at high risk for evolving resistance under managed turf systems in the United States are annual bluegrass, goosegrass, and crabgrasses. The evolution and spread of multiple herbicide resistance, an emerging threat facing the turfgrass industry, should be addressed with the use of diversified management tools. Target-site resistance has been reported commonly as a mechanism of resistance for many herbicide groups, though non–target site resistance is an emerging concern. Despite the anecdotal evidence of the mounting weed resistance issues in managed turf systems, the lack of systematic and periodic surveys at regional and national scales means that confirmed reports are very limited and sparse. Furthermore, currently available information is widely scattered in the literature. This review provides a concise summary of the current status of herbicide-resistant weeds in managed turfgrass systems in the United States and highlights key emerging threats.

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