scholarly journals Detection of Target-Site Herbicide Resistance in the Common Ragweed: Nucleotide Polymorphism Genotyping by Targeted Amplicon Sequencing

Diversity ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 118
Author(s):  
Barbara Kutasy ◽  
Zoltán Farkas ◽  
Balázs Kolics ◽  
Kincső Decsi ◽  
Géza Hegedűs ◽  
...  
Keyword(s):  
Herbicide Resistance ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Ambrosia Artemisiifolia ◽  
Target Site ◽  
Acetohydroxyacid Synthase ◽  
Wild Type ◽  
Common Ragweed ◽  
Weed Communities ◽  
Herbicide Exposure

Background: The spread of herbicide-resistance Ambrosia artemisiifolia threatens not only the production of agricultural crops, but also the composition of weed communities. The reduction of their spread would positively affect the biodiversity and beneficial weed communities in the arable habitats. Detection of resistant populations would help to reduce herbicide exposure which may contribute to the development of sustainable agroecosystems. Methods: This study focuses on the application of target-site resistance (TSR) diagnostic of A. artemisiifolia caused by different herbicides. We used targeted amplicon sequencing (TAS) on Illumina Miseq platform to detect amino acid changes in herbicide target enzymes of resistant and wild-type plants. Results: 16 mutation points of four enzymes targeted by four herbicide groups, such as Photosystem II (PSII), Acetohydroxyacid synthase (AHAS), 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) and protoporphyrinogen IX oxidase (PPO) inhibitors have been identified in common ragweed populations, so far. All the 16 mutation points were analyzed and identified. Out of these, two mutations were detected in resistant biotypes. Conclusions: The applied next-generation sequencing-targeted amplicon sequencing (NGS-TAS) method on A. artemisiifolia resistant and wild-type populations enable TSR detection of large sample numbers in a single reaction. The NGS-TAS provides information about the evolved herbicide resistance that supports the integrated weed control through the reduction of herbicide exposure which may preserve ecological properties in agroecosystems.

scholarly journals A high diversity of mechanisms endows ALS-inhibiting herbicide resistance in the invasive common ragweed (Ambrosia artemisiifolia L.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ingvild Loubet ◽  
Laëtitia Caddoux ◽  
Séverine Fontaine ◽  
Séverine Michel ◽  
Fanny Pernin ◽  
...  
Keyword(s):  
Resistance Mechanism ◽  
Resistance Management ◽  
Genotyping By Sequencing ◽  
Ambrosia Artemisiifolia ◽  
Target Site ◽  
Major Type ◽  
Common Ragweed ◽  
Resistance Evolution ◽  
Arable Weed ◽  
Target Site Resistance

AbstractAmbrosia artemisiifolia L. (common ragweed) is a globally invasive, allergenic, troublesome arable weed. ALS-inhibiting herbicides are broadly used in Europe to control ragweed in agricultural fields. Recently, ineffective treatments were reported in France. Target site resistance (TSR), the only resistance mechanism described so far for ragweed, was sought using high-throughput genotyping-by-sequencing in 213 field populations randomly sampled based on ragweed presence. Additionally, non-target site resistance (NTSR) was sought and its prevalence compared with that of TSR in 43 additional field populations where ALS inhibitor failure was reported, using herbicide sensitivity bioassay coupled with ALS gene Sanger sequencing. Resistance was identified in 46 populations and multiple, independent resistance evolution demonstrated across France. We revealed an unsuspected diversity of ALS alleles underlying resistance (9 amino-acid substitutions involved in TSR detected across 24 populations). Remarkably, NTSR was ragweed major type of resistance to ALS inhibitors. NTSR was present in 70.5% of the resistant plants and 74.1% of the fields harbouring resistance. A variety of NTSR mechanisms endowing different resistance patterns evolved across populations. Our study provides novel data on ragweed resistance to herbicides, and emphasises that local resistance management is as important as mitigating gene flow from populations where resistance has arisen.

scholarly journals Inheritance and Molecular Characterization of a Novel Mutated AHAS Gene Responsible for the Resistance of AHAS-Inhibiting Herbicides in Rapeseed (Brassica napus L.)

2020 ◽  
Vol 21 (4) ◽  
pp. 1345
Author(s):  
Qianxin Huang ◽  
Jinyang Lv ◽  
Yanyan Sun ◽  
Hongmei Wang ◽  
Yuan Guo ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Molecular Characterization ◽  
Herbicide Resistance ◽  
Acetohydroxyacid Synthase ◽  
Cross Resistance ◽  
Single Point Mutation ◽  
Wild Type ◽  
Brassica Napus L ◽  
Herbicide Resistant

The use of herbicides is an effective and economic way to control weeds, but their availability for rapeseed is limited due to the shortage of herbicide-resistant cultivars in China. The single-point mutation in the acetohydroxyacid synthase (AHAS) gene can lead to AHAS-inhibiting herbicide resistance. In this study, the inheritance and molecular characterization of the tribenuron-methyl (TBM)-resistant rapeseed (Brassica napus L.) mutant, K5, are performed. Results indicated that TBM-resistance of K5 was controlled by one dominant allele at a single nuclear gene locus. The novel substitution of cytosine with thymine at position 544 in BnAHAS1 was identified in K5, leading to the alteration of proline with serine at position 182 in BnAHAS1. The TBM-resistance of K5 was approximately 100 times that of its wild-type ZS9, and K5 also showed cross-resistance to bensufuron-methyl and monosulfuron-ester sodium. The BnAHAS1544T transgenic Arabidopsis exhibited higher TBM-resistance than that of its wild-type, which confirmed that BnAHAS1544T was responsible for the herbicide resistance of K5. Simultaneously, an allele-specific marker was developed to quickly distinguish the heterozygous and homozygous mutated alleles BnAHAS1544T. In addition, a method for the fast screening of TBM-resistant plants at the cotyledon stage was developed. Our research identified and molecularly characterized one novel mutative AHAS allele in B. napus and laid a foundation for developing herbicide-resistant rapeseed cultivars.

A Common Ragweed (Ambrosia artemisiifolia) Biotype in Southwestern Québec Resistant to Linuron

2005 ◽  
Vol 19 (3) ◽  
pp. 737-743 ◽  
Author(s):  
Sophie Saint-Louis ◽  
Antonio DiTommaso ◽  
Alan K. Watson
Keyword(s):  
Dose Rate ◽  
Herbicide Resistance ◽  
Ambrosia Artemisiifolia ◽  
Resistance Ratio ◽  
Recommended Dose ◽  
Cross Resistance ◽  
Prior History ◽  
Common Ragweed ◽  
History Of ◽  
The Common

The degree of resistance to linuron of a common ragweed biotype was investigated. Suspected linuron-resistant plants collected from a carrot field near Sherrington, Québec, were subjected to increasing rates of linuron under glasshouse conditions. Resistance to linuron of the common ragweed biotype was suspected because 33% of plants survived to reproduction after they were sprayed at a rate of 4.5 kg ai/ha, two times the dose rate recommended for linuron in carrots, and also because 3% of plants survived to reproduction after they were sprayed at a rate of 22.5 kg ai/ ha, 10 times the recommended dose. Susceptible plants collected from a field with no prior history of linuron use were all killed when sprayed at the lowest dose rate recommended, 1.125 kg ai/ha. The herbicide-resistance ratio was 29.0 for linuron, and for cross-resistance to atrazine, the ratio was 1.3, indicating that these plants exhibit greater resistance to linuron than to atrazine.

Confirmation and Resistance Mechanisms in Glyphosate-Resistant Common Ragweed (Ambrosia artemisiifolia) in Arkansas

Weed Science ◽  
2009 ◽  
Vol 57 (6) ◽  
pp. 567-573 ◽  
Author(s):  
Chad E. Brewer ◽  
Lawrence R. Oliver
Keyword(s):  
Resistance Mechanism ◽  
Population Data ◽  
Glyphosate Resistance ◽  
Population Based ◽  
Resistance Mechanisms ◽  
Ambrosia Artemisiifolia ◽  
Target Site ◽  
Susceptible Population ◽  
Common Ragweed

Greenhouse studies were established in Fayetteville, AR, to investigate glyphosate resistance in Arkansas common ragweed populations. Common ragweed seed were collected from plants in Pope and Jackson counties in Arkansas. Plants grown from seed were sprayed with one of seven glyphosate rates. Populations in Pope and Jackson counties were 21-fold and 10-fold more tolerant to glyphosate, respectively, than a known susceptible population. Based on14C-glyphosate absorption and translocation studies, reduced glyphosate absorption or translocation was not the resistance mechanism in Arkansas glyphosate-resistant common ragweed. Shikimate accumulation did not differ among the known susceptible and the two resistant populations at 3 d after treatment (DAT). However, by 5 DAT, shikimate accumulation in the two resistant populations was lower than the known susceptible population. Data indicate that glyphosate-resistant common ragweed is present in at least two locations in Arkansas, and the resistance mechanism is not an insensitive target site or reduced glyphosate absorption or translocation.

Association of the W574L ALS substitution with resistance to cloransulam and imazamox in common ragweed (Ambrosia artemisiifolia)

Weed Science ◽  
2005 ◽  
Vol 53 (4) ◽  
pp. 424-430 ◽  
Author(s):  
Danman Zheng ◽  
William L. Patzoldt ◽  
Patrick J. Tranel
Keyword(s):  
Acetolactate Synthase ◽  
Dry Weight ◽  
Ambrosia Artemisiifolia ◽  
Target Site ◽  
Common Ragweed ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Allele Specific ◽  
Treated Plant ◽  
Als Inhibitors

Previous research revealed that resistance to cloransulam in at least one population of common ragweed was conferred by an altered herbicide target site, specifically, by a tryptophan-to-leucine amino acid substitution at position 574 (W574L) of acetolactate synthase (ALS). In this study, 22 common ragweed populations, several of which were suspected cloransulam resistant, were assayed to determine if the W574L ALS substitution was correlated with resistance to ALS inhibitors. From each population, 16 greenhouse-grown plants were treated with cloransulam, and another 16 were treated with imazamox. Plant dry weights were recorded 20 d after treatment and individual plants were considered resistant if their dry weight exceeded 50% of that of nonherbicide-treated controls. For each herbicide-treated plant, allele-specific primers were used in polymerase chain reactions to determine whether the ALS alleles contained leucine or tryptophan codons at position 574. Of the 352 plants treated with cloransulam, 70 were determined to be resistant, and all but two contained one or more Leu574alleles. The frequency of imazamox resistance was much higher than that of cloransulam in the populations, with 149 of 352 plants identified as imazamox resistant. However, only about half (80) of the imazamox-resistant plants contained one or more Leu574alleles. Correlation of imazamox resistance and Leu574alleles was population dependent. ALS activity assays confirmed that imazamox resistance in plants from at least one population was due to an altered target site, even though plants from that population did not have a W574L substitution. These results lead to the conclusion that a Leu574allele is the predominant basis for cloransulam resistance in common ragweed; however, other mechanisms of resistance to ALS inhibitors exist in some populations.

Decoding Non-Target-Site Herbicide Resistance in Sunflower: The Beginning of the Story

Helia ◽  
2019 ◽  
Vol 42 (70) ◽  
pp. 1-16
Author(s):  
Mercedes Gil ◽  
Graciela Nestares
Keyword(s):  
Weed Control ◽  
Herbicide Resistance ◽  
Weed Management ◽  
Management Strategies ◽  
Target Site ◽  
Acetohydroxyacid Synthase ◽  
Cross Resistance ◽  
Resistance To Herbicides ◽  
Transgenic Technologies ◽  
New Compounds

AbstractIn the last years, many efforts have been made to develop sunflower cultivars showing important agronomical characteristics such as herbicide resistance. These approaches have been focused mainly on resistance to herbicides with the same mode of action, that is acetohydroxyacid synthase (AHAS) inhibitors. To date, four induced and natural AHAS mutations have been found that confer resistance to these herbicides and many of these alleles are being used for the production of sunflower hybrids resistant to herbicides and to develop different non-transgenic technologies for weed control. However, little is known about the bases of non-target-site-based resistance (NTSR) developing cross-resistance to herbicides with different modes of action in sunflower. These mechanisms diminish the number of active herbicide molecules that reach the target and are generally polygenic. Elucidating the nature of NTSR would allow evaluating maximal efficiency conditions for the herbicide and would enable to establish weed management strategies in sunflower crop. Nowadays, mining of NTSR genes can be more easily accomplished taking advantage of up-to-date omics-based approaches: high-throughput techniques involving genomics, transcriptomics, proteomics and metabolomics. Considering the difficulties in the discovery of new compounds with a broad spectrum of weed control, it results essential to broaden the use of former herbicides which are highly efficient and ecologically desirable. Full understanding of NTSR mechanisms in sunflower would allow detecting specific genes potentially useful as biotechnological tools for the phytoremediation of herbicides and modern plant breeding.

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 Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures

Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 569
Author(s):  
Chakriya Sansupa ◽  
Sara Fareed Mohamed Wahdan ◽  
Terd Disayathanoowat ◽  
Witoon Purahong
Keyword(s):  
Bacterial Community ◽  
Forest Soil ◽  
Culture Media ◽  
Enrichment Culture ◽  
Sequence Similarity ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Soil Samples ◽  
Enrichment Cultures ◽  
Total Community

This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.

Investigating the resistance levels and mechanisms to penoxsulam and cyhalofop-butyl in barnyardgrass (Echinochloa crus-galli) from Ningxia province, China

Weed Science ◽  
2021 ◽  
pp. 1-25
Author(s):  
Qian Yang ◽  
Xia Yang ◽  
Zichang Zhang ◽  
Jieping Wang ◽  
Weiguo Fu ◽  
...  
Keyword(s):  
Herbicide Resistance ◽  
Molecular Mechanisms ◽  
Acetolactate Synthase ◽  
Rice Fields ◽  
Target Site ◽  
Herbicide Resistant ◽  
Susceptible Populations ◽  
High Level ◽  
Als Inhibitor ◽  
Encoding Genes

Abstract Barnyardgrass (Echinochloa crus-galli) is a noxious grass weed which infests rice fields and causes huge crop yield losses. In this study, we collected twelve E. crus-galli populations from rice fields of Ningxia province in China and investigated the resistance levels to acetolactate synthase (ALS) inhibitor penoxsulam and acetyl-CoA carboxylase (ACCase) inhibitor cyhalofop-butyl. The results showed that eight populations exhibited resistance to penoxsulam and four populations evolved resistance to cyhalofop-butyl. Moreover, all of the four cyhalofop-butyl-resistant populations (NX3, NX4, NX6 and NX7) displayed multiple-herbicide-resistance (MHR) to both penoxsulam and cyhalofop-butyl. The alternative herbicides bispyribac-sodium, metamifop and fenoxaprop-P-ethyl cannot effectively control the MHR plants. To characterize the molecular mechanisms of resistance, we amplified and sequenced the target-site encoding genes in resistant and susceptible populations. Partial sequences of three ALS genes and six ACCase genes were examined. A Trp-574-Leu mutation was detected in EcALS1 and EcALS3 in two high-level (65.84- and 59.30-fold) penoxsulam-resistant populations NX2 and NX10, respectively. In addition, one copy (EcACC4) of ACCase genes encodes a truncated aberrant protein due to a frameshift mutation in E. crus-galli populations. None of amino acid substitutions that are known to confer herbicide resistance were detected in ALS and ACCase genes of MHR populations. Our study reveals the widespread of multiple-herbicide resistant E. crus-galli populations at Ningxia province of China that exhibit resistance to several ALS and ACCase inhibitors. Non-target-site based mechanisms are likely to be involved in E. crus-galli resistance to the herbicides, at least in four MHR populations.

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