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Li Q, Wang H, Yu J, Zhang W, Guo W, Liu Y. Metabolism-Based Herbicide Resistance to Mesosulfuron-methyl and Identification of Candidate Genes in Bromus japonicus. PLANTS (BASEL, SWITZERLAND) 2024; 13:1751. [PMID: 38999592 PMCID: PMC11244151 DOI: 10.3390/plants13131751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/20/2024] [Accepted: 06/22/2024] [Indexed: 07/14/2024]
Abstract
The evolved resistance of Bromus japonicus Houtt. to ALS-inhibiting herbicides is well established. Previous studies have primarily focused on target-site resistance; however, non-target-site resistance has not been well characterized. This investigation demonstrated that ALS gene sequencing did not detect any previously known resistance mutations in a mesosulfuron-methyl-resistant (MR) population, and notably, treatment with the P450 monooxygenase (P450) inhibitor malathion markedly heightened susceptibility to mesosulfuron-methyl. Utilizing UPLC-MS/MS analysis confirmed elevated mesosulfuron-methyl metabolism in MR plants. The integration of Isoform Sequencing (Iso-Seq) and RNA Sequencing (RNA-Seq) facilitated the identification of candidate genes associated with non-target sites in a subpopulation with two generations of herbicide selection. Through qRT-PCR analysis, 21 differentially expressed genes were characterized, and among these, 10 genes (comprising three P450s, two glutathione S-transferases, one glycosyltransferase, two ATP-binding cassette transporters, one oxidase, and one hydrolase) exhibited constitutive upregulation in resistant plants. Our findings substantiated that increased herbicide metabolism is a driving force behind mesosulfuron-methyl resistance in this B. japonicus population.
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Affiliation(s)
- Qi Li
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Hengzhi Wang
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Jinping Yu
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Wei Zhang
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Wenlei Guo
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yixue Liu
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
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Chen K, Yang H, Wu D, Peng Y, Lian L, Bai L, Wang L. Weed biology and management in the multi-omics era: Progress and perspectives. PLANT COMMUNICATIONS 2024; 5:100816. [PMID: 38219012 PMCID: PMC11009161 DOI: 10.1016/j.xplc.2024.100816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/20/2023] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
Weeds pose a significant threat to crop production, resulting in substantial yield reduction. In addition, they possess robust weedy traits that enable them to survive in extreme environments and evade human control. In recent years, the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy traits. In this review, we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology, including the origins of weed species, weed classification, and the underlying genetic and molecular bases of important weedy traits such as crop-weed interactions, adaptability to different environments, photoperiodic flowering responses, and herbicide resistance. In addition, we discuss limitations to the application of multi-omics techniques in weed science, particularly compared with their extensive use in model plants and crops. In this regard, we provide a forward-looking perspective on the future application of multi-omics technologies to weed science research. These powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy traits. The resulting advances will facilitate the development of sustainable and highly effective weed management strategies, promoting greener practices in agriculture.
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Affiliation(s)
- Ke Chen
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Haona Yang
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Di Wu
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Yajun Peng
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Lei Lian
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao 266000, China
| | - Lianyang Bai
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou 510715, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| | - Lifeng Wang
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou 510715, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
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Sehgal D, Oliveira C, Mathioni S, Widdison S, Plumb W, Campos B, Kaundun SS. Genomic characterisation and dissection of the onset of resistance to acetyl CoA carboxylase-inhibiting herbicides in a large collection of Digitaria insularis from Brazil. Front Genet 2024; 15:1340852. [PMID: 38440194 PMCID: PMC10910277 DOI: 10.3389/fgene.2024.1340852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 01/19/2024] [Indexed: 03/06/2024] Open
Abstract
An in-depth genotypic characterisation of a diverse collection of Digitaria insularis was undertaken to explore the neutral genetic variation across the natural expansion range of this weed species in Brazil. With the exception of Minas Gerais, populations from all other states showed high estimates of expected heterozygosity (HE > 0.60) and genetic diversity. There was a lack of population structure based on geographic origin and a low population differentiation between populations across the landscape as evidenced by average Fst value of 0.02. On combining haloxyfop [acetyl CoA carboxylase (ACCase)-inhibiting herbicide] efficacy data with neutral genetic variation, we found evidence of presence of two scenarios of resistance evolution in this weed species. Whilst populations originating from north-eastern region demonstrated an active role of gene flow, populations from the mid-western region displayed multiple, independent resistance evolution as the major evolutionary mechanism. A target-site mutation (Trp2027Cys) in the ACCase gene, observed in less than 1% of resistant populations, could not explain the reduced sensitivity of 15% of the populations to haloxyfop. The genetic architecture of resistance to ACCase-inhibiting herbicides was dissected using a genome wide association study (GWAS) approach. GWAS revealed association of three SNPs with reduced sensitivity to haloxyfop and clethodim. In silico analysis of these SNPs revealed important non-target site genes belonging to families involved in herbicide detoxification, including UDPGT91C1 and GT2, and genes involved in vacuolar sequestration-based degradation pathway. Exploration of five genomic prediction models revealed that the highest prediction power (≥0.80) was achieved with the models Bayes A and RKHS, incorporating SNPs with additive effects and epistatic interactions, respectively.
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Affiliation(s)
- Deepmala Sehgal
- Syngenta Ltd., Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Claudia Oliveira
- Syngenta Crop Protection, Holambra Research and Development Center, São Paulo, Brazil
| | - Sandra Mathioni
- Syngenta Crop Protection, Holambra Research and Development Center, São Paulo, Brazil
| | - Stephanie Widdison
- Syngenta Ltd., Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Will Plumb
- Syngenta Ltd., Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Breno Campos
- Syngenta Ltd., Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Shiv Shankhar Kaundun
- Syngenta Ltd., Jealott’s Hill International Research Centre, Bracknell, United Kingdom
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Lu B, Meng R, Wang Y, Xiong W, Ma Y, Gao P, Ren J, Zhang L, Zhao Z, Fan G, Wen Y, Yuan X. Distinctive physiological and molecular responses of foxtail millet and maize to nicosulfuron. FRONTIERS IN PLANT SCIENCE 2024; 14:1308584. [PMID: 38293619 PMCID: PMC10824897 DOI: 10.3389/fpls.2023.1308584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/29/2023] [Indexed: 02/01/2024]
Abstract
Introduction Nicosulfuron is the leading acetolactate synthase inhibitor herbicide product, and widely used to control gramineous weeds. Here, we investigated the metabolic process of nicosulfuron into foxtail millet and maize, in order to clarify the mechanism of the difference in sensitivity of foxtail millet and maize to nicosulfuron from the perspective of physiological metabolism and provide a theoretical basis for the breeding of nicosulfuron-resistant foxtail millet varieties. Methods We treated foxtail millet (Zhangzagu 10, Jingu 21) and maize (Nongda 108, Ditian 8) with various doses of nicosulfuron in both pot and field experiments. The malonaldehyde (MDA) content, target enzymes, detoxification enzymes, and antioxidant enzymes, as well as related gene expression levels in the leaf tissues of foxtail millet and maize were measured, and the yield was determined after maturity. Results The results showed that the recommended dose of nicosulfuron caused Zhangzagu 10 and Jingu 21 to fail to harvest; the yield of the sensitive maize variety (Ditian 8) decreased by 37.09%, whereas that of the resistant maize variety (Nongda 108) did not decrease. Nicosulfuron stress increased the CYP450 enzyme activity, MDA content, and antioxidant enzyme activity of foxtail millet and maize, reduced the acetolactate synthase (ALS) activity and ALS gene expression of foxtail millet and Ditian 8, and reduced the glutathione S-transferase (GST) activity and GST gene expression of foxtail millet. In conclusion, target enzymes, detoxification enzymes, and antioxidant enzymes were involved in the detoxification metabolism of nicosulfuron in plants. ALS and GST are the main factors responsible for the metabolic differences among foxtail millet, sensitive maize varieties, and resistant maize varieties. Discussion These findings offer valuable insights for exploring the target resistance (TSR) and non-target resistance (NTSR) mechanisms in foxtail millet under herbicide stress and provides theoretical basis for future research of develop foxtail millet germplasm with diverse herbicide resistance traits.
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Affiliation(s)
- Boyu Lu
- State Key Laboratory of Sustainable Dryland Agriculture (in preparation), Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Ru Meng
- State Key Laboratory of Sustainable Dryland Agriculture (in preparation), Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Yiru Wang
- State Key Laboratory of Sustainable Dryland Agriculture (in preparation), Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Wei Xiong
- State Key Laboratory of Sustainable Dryland Agriculture (in preparation), Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Yuchao Ma
- State Key Laboratory of Sustainable Dryland Agriculture (in preparation), Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Peng Gao
- State Key Laboratory of Sustainable Dryland Agriculture (in preparation), Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Jianhong Ren
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Liguang Zhang
- State Key Laboratory of Sustainable Dryland Agriculture (in preparation), Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Zhihai Zhao
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Guangyu Fan
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Yinyuan Wen
- State Key Laboratory of Sustainable Dryland Agriculture (in preparation), Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Xiangyang Yuan
- State Key Laboratory of Sustainable Dryland Agriculture (in preparation), Shanxi Agricultural University, Taiyuan, Shanxi, China
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Akbarabadi A, Ismaili A, Nazarian Firouzabadi F, Ercisli S, Kahrizi D. Assessment of ACC and P450 Genes Expression in Wild Oat (Avena ludoviciana) in Different Tissues Under Herbicide Application. Biochem Genet 2023; 61:1867-1879. [PMID: 36877417 DOI: 10.1007/s10528-023-10357-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 02/15/2023] [Indexed: 03/07/2023]
Abstract
Target-site resistance (TSR) and non-target-site resistance (NTSR) to herbicides in arable weeds are increasing rapidly all over the world and threatening universal food safety. Resistance to herbicides that inhibit ACCase activity has been identified in wild oat. In this study, expression of ACC1, ACC2, CYP71R4 and CYP81B1 genes under herbicide stress conditions were studied in two TSR (resistant in the residue Ile1781-Leu and Ile2041-Asn of ACCase) biotypes, two NTSR biotypes and one susceptible biotype of A. ludoviciana for the first time. Treated and untreated biotypes with ACCase-inhibitor clodinafop propargyl herbicide were sampled from the stem and leaf tissues at 24 h after treatment. Our results showed an increase in gene expression levels in different tissues of both types of resistance biotypes that occurred under herbicide treatment compared with non-herbicide treatment. In all samples, the expression levels of leaf tissue in all studied genes were higher than in stem tissue. The results of ACC gene expression showed that the expression level of ACC1 was significantly higher than that of ACC2. Also, expression levels of TSR biotypes were higher than NTSR biotypes for the ACC1 gene. For both CYP71R4 and CYP81B1 genes, the expression ratio increased significantly in TSR and NTSR biotypes in different tissues after herbicide treatment. In contrast, the expression levels of CYP genes in NTSR biotypes were higher than in TSR biotypes. Our results support the hypothesis that the reaction of plants to herbicide is carried out through a different regulation of genes, which can be the result of the interaction of resistance type in the target or non-target-site.
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Affiliation(s)
- Ali Akbarabadi
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Ahmad Ismaili
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Farhad Nazarian Firouzabadi
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, 25240, Erzurum, Turkey
| | - Danial Kahrizi
- Department of Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
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Casey A, Köcher T, Caygill S, Champion C, Bonnot C, Dolan L. Transcriptome changes in chlorsulfuron-treated plants are caused by acetolactate synthase inhibition and not induction of a herbicide detoxification system in Marchantia polymorpha. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 191:105370. [PMID: 36963939 DOI: 10.1016/j.pestbp.2023.105370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/02/2023] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
A sensing mechanism in mammals perceives xenobiotics and induces the transcription of genes encoding proteins that detoxify these molecules. However, it is unclear if plants sense xenobiotics, and activate an analogous signalling system leading to their detoxification. Using the liverwort Marchantia polymorpha, we tested the hypothesis that there is a sensing system in plants that perceives herbicides resulting in the increased transcription of genes encoding proteins that detoxify these herbicides. Consistent with the hypothesis, we show that chlorsulfuron-treatment induces changes in the M. polymorpha transcriptome. However, these transcriptome changes do not occur in chlorsulfuron (CS)-treated target site resistant mutants, where the gene encoding the target carries a mutation that confers resistance to chlorsulfuron. Instead, we show that inactivation of the chlorsulfuron target, acetolactate synthase (ALS) (also known as acetohydroxyacid synthase (AHAS)), is required for the transcriptome response. These data demonstrate that the transcriptome changes in chlorsulfuron-treated plants are caused by disrupted amino acid synthesis and metabolism resulting from acetolactate synthase inhibition, and indicate that the transcriptome changes are not caused by a herbicide sensing mechanism.
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Affiliation(s)
- Alexandra Casey
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom; Gregor Mendel Institute, Dr. Bohr-Gasse, 3, Vienna 1030, Austria
| | - Thomas Köcher
- Vienna BioCenter Core Facilities GmbH, Dr. Bohr-Gasse 3, Vienna 1030, Austria
| | - Samuel Caygill
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom; Gregor Mendel Institute, Dr. Bohr-Gasse, 3, Vienna 1030, Austria
| | - Clément Champion
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Clémence Bonnot
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Liam Dolan
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom; Gregor Mendel Institute, Dr. Bohr-Gasse, 3, Vienna 1030, Austria.
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Li Q, Zhao N, Jiang M, Wang M, Zhang J, Cao H, Liao M. Metamifop resistance in Echinochloa glabrescens via glutathione S-transferases-involved enhanced metabolism. PEST MANAGEMENT SCIENCE 2023. [PMID: 36914944 DOI: 10.1002/ps.7453] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/07/2023] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Echinochloa glabrescens Munro ex Hook. f. is one of the main Echinochloa spp. seriously invading Chinese rice fields and has evolved resistance to commonly used herbicides. Previously, an E. glabrescens population (LJ-02) with suspected resistance to the acetyl-CoA carboxylase (ACCase)-inhibiting herbicide metamifop was collected. This study aimed to determine its resistance status to metamifop and investigate the internal molecular mechanisms of resistance. RESULTS Single-dose testing confirmed that the LJ-02 population had evolved resistance to metamifop. Gene sequencing and a relative expression assay of ACCase ruled out target-site based resistance to metamifop in LJ-02. Whole-plant bioassays revealed that, compared with the susceptible population XZ-01, LJ-02 was highly resistant to metamifop and exhibited cross-resistance to fenoxaprop-P-ethyl. Pretreatment with the known glutathione S-transferase (GST) inhibitor, 4-chloro-7-nitrobenzoxadiazole (NBD-Cl), largely reversed the resistance to metamifop by approximately 81%. Liquid chromatography-tandem mass spectrometry analysis indicated that the metabolic rates of one of the major metabolites of metamifop, N-(2-fluorophenyl)-2-hydroxy-N-methylpropionamide (HPFMA), were up to 383-fold faster in LJ-02 plants than in XZ-01 plants. There were higher basal and metamifop-inducible GST activities toward 1-chloro-2,4-dinitrobenzene (CDNB) in LJ-02 than in XZ-01. Six GST genes were metamifop-induced and overexpressed in the resistant LJ-02 population. CONCLUSION This study reports, for the first time, the occurrence of metabolic metamifop resistance in E. glabrescens worldwide. The high-level metamifop resistance in the LJ-02 population may mainly involve specific isoforms of GSTs that endow high catalytic activity and strong substrate specificity. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Qi Li
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Ning Zhao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Minghao Jiang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Mali Wang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Jingxu Zhang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Haiqun Cao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Min Liao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
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Plant Metabolomics: An Overview of the Role of Primary and Secondary Metabolites against Different Environmental Stress Factors. Life (Basel) 2023; 13:life13030706. [PMID: 36983860 PMCID: PMC10051737 DOI: 10.3390/life13030706] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/02/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Several environmental stresses, including biotic and abiotic factors, adversely affect the growth and development of crops, thereby lowering their yield. However, abiotic factors, e.g., drought, salinity, cold, heat, ultraviolet radiations (UVr), reactive oxygen species (ROS), trace metals (TM), and soil pH, are extremely destructive and decrease crop yield worldwide. It is expected that more than 50% of crop production losses are due to abiotic stresses. Moreover, these factors are responsible for physiological and biochemical changes in plants. The response of different plant species to such stresses is a complex phenomenon with individual features for several species. In addition, it has been shown that abiotic factors stimulate multi-gene responses by making modifications in the accumulation of the primary and secondary metabolites. Metabolomics is a promising way to interpret biotic and abiotic stress tolerance in plants. The study of metabolic profiling revealed different types of metabolites, e.g., amino acids, carbohydrates, phenols, polyamines, terpenes, etc, which are accumulated in plants. Among all, primary metabolites, such as amino acids, carbohydrates, lipids polyamines, and glycine betaine, are considered the major contributing factors that work as osmolytes and osmoprotectants for plants from various environmental stress factors. In contrast, plant-derived secondary metabolites, e.g., phenolics, terpenoids, and nitrogen-containing compounds (alkaloids), have no direct role in the growth and development of plants. Nevertheless, such metabolites could play a significant role as a defense by protecting plants from biotic factors such as herbivores, insects, and pathogens. In addition, they can enhance the resistance against abiotic factors. Therefore, metabolomics practices are becoming essential and influential in plants by identifying different phytochemicals that are part of the acclimation responses to various stimuli. Hence, an accurate metabolome analysis is important to understand the basics of stress physiology and biochemistry. This review provides insight into the current information related to the impact of biotic and abiotic factors on variations of various sets of metabolite levels and explores how primary and secondary metabolites help plants in response to these stresses.
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Sun Y, Han Y, Ma H, Wei S, Lan Y, Cao Y, Huang H, Huang Z. First Report of the Molecular Mechanism of Resistance to Tribenuron-Methyl in Silene conoidea L. PLANTS (BASEL, SWITZERLAND) 2022; 11:3044. [PMID: 36432773 PMCID: PMC9692542 DOI: 10.3390/plants11223044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Silene conoidea L. is an annual troublesome broadleaf weed in winter wheat fields in China. In recent years, field applications of tribenuron-methyl have been ineffective in controlling S. conoidea in Hebei Province, China. The aim of this study was to determine the molecular basis of tribenuron-methyl resistance in S. conoidea. Whole-plant response assays revealed that the resistant population (R) exhibited a higher level of resistance (382.3-fold) to tribenuron-methyl. The R population also showed high cross-resistance to other acetolactate synthase (ALS) inhibitors, including imazethapyr, bispyribac-sodium and florasulam. However, the R population could be controlled by the field-recommended rates of bentazone, MCPA, fluroxypyr, carfentrazone-ethyl and bromoxynil. In vitro ALS activity assays indicated that the tribenuron-methyl I50 value for the R population was 18.5 times higher than those for the susceptible population (S). ALS gene sequencing revealed an amino acid mutation, Trp-574-Leu, in the R population. Pretreatment with the P450 inhibitor malathion indicated that the R population might have cytochrome P450-mediated metabolic resistance. These results suggest that the Trp-574-Leu mutation and P450-mediated enhanced metabolism coexist in S. conoidea to generate tribenuron-methyl resistance. This is the first time that target-site and non-target-site resistance to tribenuron-methyl has been reported in S. conoidea.
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Affiliation(s)
- Ying Sun
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Yujun Han
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Hong Ma
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Shouhui Wei
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuning Lan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yi Cao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hongjuan Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhaofeng Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Yang J, Yu H, Cui H, Chen J, Li X. PsbA gene over-expression and enhanced metabolism conferring resistance to atrazine in Commelina communis. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 188:105260. [PMID: 36464365 DOI: 10.1016/j.pestbp.2022.105260] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/25/2022] [Accepted: 10/07/2022] [Indexed: 06/17/2023]
Abstract
Commelina communis L. is a troublesome weed in agronomic fields and increasingly threatens the yield security of corn in north-eastern China. Previously, we found that a C. communis population (JL-1) has evolved resistance to atrazine. Although the potential genetic and enzymic differences contributing to atrazine resistance in this population have been investigated, the specific molecular mechanisms underlying C. communis resistance are still poorly understood. Here, the expression level of the target gene PsbA and the non-target-site resistance (NTSR) mechanism for this population were studied. The results showed that the decline in chlorophyll content in JL-1 leaves was less than in the susceptible JS-10 population following atrazine treatment. JL-1 exhibited an enhanced expression of the PsbA gene compared with JS-10 of 7.28- and 14.28-fold higher at 0 and 24 h after treatment with atrazine, respectively. The cytochrome P450 monooxygenase (P450) inhibitor piperonyl butoxide (PBO) increased the phytotoxicity of atrazine in both populations of C. communis. Seven candidate genes associated with NTSR of Jl-1 were identified through RNA-seq and validated by quantitative real-time PCR, including 5 upregulated genes involved in herbicide metabolism. In addition, the activities of glutathione S-transferases and P450s in JL-1 were increased compared with JS-10. Collectively, PsbA gene overexpression and enhanced metabolism are likely to be responsible for JL-1 resistance to atrazine.
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Affiliation(s)
- Juan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Hebei Key Laboratory of Crop Stress Biology (in Preparation), Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Haiyan Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hailan Cui
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jingchao Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiangju Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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11
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Zhang D, Li X, Bei F, Jin T, Jia S, Bu R, Wang J, Wang H, Liu W. Investigating the Metabolic Mesosulfuron-Methyl Resistance in Aegilops tauschii Coss. By Transcriptome Sequencing Combined with the Reference Genome. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11429-11440. [PMID: 36048004 DOI: 10.1021/acs.jafc.2c04529] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Aegilops tauschii Coss. is a malignant weed in wheat fields in China, its herbicide resistance has been threatening crop production. This study identified one mesosulfuron-methyl-resistant(R) population, JJMHN2018-05 (R), without target resistance mutations. To fully understand the resistance mechanism, non-target site resistance was investigated by using transcriptome sequencing combined with a reference genome. Results showed that the cytochrome P450 monooxygenase (P450) inhibitor malathion significantly increased the mesosulfuron-methyl sensitivity in R plants, and greater herbicide-induced glutathione S-transferase (GST) activity was also confirmed. Liquid chromatography with tandem mass spectrometry analysis further supported the enhanced mesosulfuron-methyl metabolism in R plants. Gene expression data analysis and qRT-PCR validation indicated that eight P450s, six GSTs, two glycosyltransferases (GTs), four peroxidases, and one aldo-keto reductase (AKRs) stably upregulated in R plants. This research demonstrates that the P450s and GSTs involved in enhanced mesosulfuron-methyl metabolism contribute to mesosulfuron-methyl resistance in A. tauschii and identifies potential contributors from metabolic enzyme families.
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Affiliation(s)
- Dawei Zhang
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xiangju Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Feng Bei
- Tai'an Customs, Tai'an 271000, Shandong, PR China
| | - Tao Jin
- Qingdao Kingagroot Chemical Compound Co., Ltd., Qingdao 266000, PR China
| | - Sisi Jia
- Tai'an Customs, Tai'an 271000, Shandong, PR China
| | - Ruotong Bu
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Jinxin Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Hengzhi Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Weitang Liu
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China
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12
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Diversity of Herbicide-Resistance Mechanisms of Avena fatua L. to Acetyl-CoA Carboxylase-Inhibiting Herbicides in the Bajio, Mexico. PLANTS 2022; 11:plants11131644. [PMID: 35807596 PMCID: PMC9269088 DOI: 10.3390/plants11131644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022]
Abstract
Herbicide resistance is an evolutionary process that affects entire agricultural regions’ yield and productivity. The high number of farms and the diversity of weed management can generate hot selection spots throughout the regions. Resistant biotypes can present a diversity of mechanisms of resistance and resistance factors depending on selective conditions inside the farm; this situation is similar to predictions by the geographic mosaic theory of coevolution. In Mexico, the agricultural region of the Bajio has been affected by herbicide resistance for 25 years. To date, Avena fatua L. is one of the most abundant and problematic weed species. The objective of this study was to determine the mechanism of resistance of biotypes with failures in weed control in 70 wheat and barley crop fields in the Bajio, Mexico. The results showed that 70% of farms have biotypes with target site resistance (TSR). The most common mutations were Trp–1999–Cys, Asp–2078–Gly, Ile–2041–Asn, and some of such mutations confer cross-resistance to ACCase-inhibiting herbicides. Metabolomic fingerprinting showed four different metabolic expression patterns. The results confirmed that in the Bajio, there exist multiple selection sites for both resistance mechanisms, which proves that this area can be considered as a geographic mosaic of resistance.
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13
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Zhao N, Yan Y, Liu W, Wang J. Cytochrome P450 CYP709C56 metabolizing mesosulfuron-methyl confers herbicide resistance in Alopecurus aequalis. Cell Mol Life Sci 2022; 79:205. [PMID: 35334005 PMCID: PMC11072224 DOI: 10.1007/s00018-022-04171-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 12/15/2022]
Abstract
Multiple herbicide resistance in diverse weed species endowed by enhanced herbicide detoxification or degradation is rapidly growing into a great threat to herbicide sustainability and global food safety. Although metabolic resistance is frequently documented in the economically damaging arable weed species shortawn foxtail (Alopecurus aequalis Sobol.), relevant molecular knowledge has been lacking. Previously, we identified a field population of A. aequalis (R) that had evolved metabolic resistance to the commonly used acetolactate synthase (ALS)-inhibiting herbicide mesosulfuron-methyl. RNA sequencing was used to discover potential herbicide metabolism-related genes, and four cytochrome P450s (CYP709C56, CYP71R18, CYP94C117, and CYP94E14) were identified with higher expressions in the R vs. susceptible (S) plants. Here the full-length P450 complementary DNA transcripts were each cloned with identical sequences between the S and R plants. Transgenic Arabidopsis overexpressing CYP709C56 became resistant to the sulfonylurea herbicide mesosulfuron-methyl and the triazolo-pyrimidine herbicide pyroxsulam. This resistance profile generally but does not completely in accordance with what is evident in the R A. aequalis. Transgenic lines exhibited enhanced capacity for detoxifying mesosulfuron-methyl into O-demethylated metabolite, which is in line with the detection of O-demethylated herbicide metabolite in vitro in transformed yeast. Structural modeling predicted that mesosulfuron-methyl binds to CYP709C56 involving amino acid residues Thr-328, Thr-500, Asn-129, Gln-392, Phe-238, and Phe-242 for achieving O-demethylation. Constitutive expression of CYP709C56 was highly correlated with the metabolic mesosulfuron-methyl resistance in A. aequalis. These results indicate that CYP709C56 degrades mesosulfuron-methyl and its up-regulated expression in A. aequalis confers resistance to mesosulfuron-methyl.
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Affiliation(s)
- Ning Zhao
- Anhui Province Key Laboratory of Integrated Pest Management On Crops, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
- College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China
| | - Yanyan Yan
- College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China
| | - Weitang Liu
- College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China.
| | - Jinxin Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China.
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14
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Zhao N, Yang J, Jiang M, Liao M, Cao H. Identification of essential genes involved in metabolism-based resistance mechanism to fenoxaprop-P-ethyl in Polypogon fugax. PEST MANAGEMENT SCIENCE 2022; 78:1164-1175. [PMID: 34821014 DOI: 10.1002/ps.6733] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/11/2021] [Accepted: 11/24/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Metabolic resistance is a worldwide concern for weed control but has not yet been well-characterized at the genetic level. Previously, we have identified an Asia minor bluegrass (Polypogon fugax Nees ex Steud.) population AHHY exhibiting cytochrome P450 (P450)-involved metabolic resistance to fenoxaprop-P-ethyl. In this study, we aimed to confirm the metabolic fenoxaprop-P-ethyl resistance in AHHY and uncover the potential herbicide metabolism-related genes in this economically damaging weed species. RESULTS Liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays indicated the metabolic rates of fenoxaprop-P-ethyl were significantly faster in resistant (R, AHHY) than in susceptible (S, SDTS) plants. The amount of phytotoxic fenoxaprop-P peaked at 12 h after herbicide treatment (HAT) and started to decrease at 24 HAT in both biotypes. R and S plants at 24 HAT were sampled to conduct isoform-sequencing (Iso-Seq) and RNA-sequencing (RNA-Seq). A reference transcriptome containing 24 972 full-length isoforms was obtained, of which 24 329 unigenes were successfully annotated. Transcriptomic profiling identified 28 detoxifying enzyme genes constitutively and/or herbicide-induced up-regulated in R than in S plants. Real-time quantitative polymerase chain reaction (RT-qPCR) confirmed 17 genes were consistently up-regulated in R and its F1 generation plants. They were selected as potential fenoxaprop-P-ethyl metabolism-related genes, including ten P450s, one glutathione-S-transferase, one UDP-glucosyltransferase, and five adenosine triphosphate (ATP)-binding cassette transporters. CONCLUSION This study revealed that the enhanced rates of fenoxaprop-P-ethyl metabolism in P. fugax were very likely driven by the herbicide metabolism-related genes. The transcriptome data generated by Iso-Seq combined with RNA-Seq will provide abundant gene resources for understanding the molecular mechanisms of resistance in P. fugax.
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Affiliation(s)
- Ning Zhao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Jiajia Yang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Minghao Jiang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Min Liao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Haiqun Cao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
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15
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Wang J, Cao W, Guo Q, Yang Y, Bai L, Pan L. Resistance to mesosulfuron-methyl in Beckmannia syzigachne may involve ROS burst and non-target-site resistance mechanisms. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 229:113072. [PMID: 34922171 DOI: 10.1016/j.ecoenv.2021.113072] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 12/03/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Herbicide resistance to chemical herbicide is a global issue that presents an ongoing threat to grain production. Though it has been frequently implicated that the production of detoxification enzymes increased in resistance development, the mechanisms for overexpression of these genes employed by herbicide-resistant weeds remain complicated. In this study, a mesosulfuron-methyl resistant Beckmannia syzigachne population (R) was found to be cross-resistant to another herbicide pyriminobac-methyl. No known target-site mutations were detected in the R population. In contrast, the decreased uptake and enhanced metabolic rates of mesosulfuron-methyl were detected in the R than the susceptible (S) population. Two candidate ATP-binding cassette (ABC) transporter genes (ABCB25 and ABCC14) that were constitutively up-regulated in the R population were identified by RNA-sequencing and validated by RT-qPCR. Alteration of antioxidant enzyme activities and gene expressions implied that mesosulfuron-methyl-induced antioxidant defenses provoked reactive oxygen species (ROS) burst. ROS scavenger assay showed that ROS induces ABCB25 and ABCC14 expression. This study reported for the first time that ABC transporters mediated non-target-site resistance contributes to mesosulfuron-methyl resistance in a B. syzigachne population, and implicated that ROS burst might be involved in the overexpression of ABC transporter genes in weeds.
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Affiliation(s)
- Junzhi Wang
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, Graduate School of Hunan University, Changsha 410125, China
| | - Wanfen Cao
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Qiushuang Guo
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Yang Yang
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Lianyang Bai
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, Graduate School of Hunan University, Changsha 410125, China.
| | - Lang Pan
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China.
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16
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Laforest M, Soufiane B, Patterson EL, Vargas JJ, Boggess SL, Houston LC, Trigiano RN, Brosnan JT. Differential expression of genes associated with non-target site resistance in Poa annua with target site resistance to acetolactate synthase inhibitors. PEST MANAGEMENT SCIENCE 2021; 77:4993-5000. [PMID: 34218510 PMCID: PMC8518846 DOI: 10.1002/ps.6541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 06/28/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Poa annua is a pervasive grassy, self-pollinating, weed that has evolved resistance to 10 different herbicide modes-of-action, third most of all weed species. We investigated constitutive overexpression of genes associated with non-target site resistance (NTSR) in POAAN-R3 and the response of those genes when treated with trifloxysulfuron despite the biotype having a known target site mutation in acetolactate synthase (ALS). RESULTS Despite having an ALS target site mutation, POAAN-R3 still had a transcriptomic response to herbicide application that differed from a susceptible biotype. We observed differential expression of genes associated with transmembrane transport and oxidation-reduction activities, with differences being most pronounced prior to herbicide treatment. CONCLUSIONS In the P. annua biotype we studied with confirmed target site resistance to ALS inhibitors, we also observed constitutive expression of genes regulating transmembrane transport, as well as differential expression of genes associated with oxidative stress after treatment with trifloxysulfuron. This accumulation of mechanisms, in addition to the manifestation of target site resistance, could potentially increase the chance of survival when plants are challenged by different modes of action.
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Affiliation(s)
- Martin Laforest
- Saint‐Jean‐sur‐Richelieu R&D Centre, Agriculture and Agri‐Food CanadaSaint‐Jean‐sur‐RichelieuQCCanada
| | - Brahim Soufiane
- Saint‐Jean‐sur‐Richelieu R&D Centre, Agriculture and Agri‐Food CanadaSaint‐Jean‐sur‐RichelieuQCCanada
| | - Eric L Patterson
- Department of Plant, Soil, & Microbial SciencesMichigan State UniversityEast LansingMIUSA
| | - José J Vargas
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Sarah L Boggess
- Department of Entomology & Plant PathologyUniversity of TennesseeKnoxvilleTNUSA
| | - Logan C Houston
- Department of Entomology & Plant PathologyUniversity of TennesseeKnoxvilleTNUSA
| | - Robert N Trigiano
- Department of Entomology & Plant PathologyUniversity of TennesseeKnoxvilleTNUSA
| | - James T Brosnan
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
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Yang Y, Gardner C, Gupta P, Peng Y, Piasecki C, Millwood RJ, Ahn TH, Stewart CN. Novel Candidate Genes Differentially Expressed in Glyphosate-Treated Horseweed ( Conyza canadensis). Genes (Basel) 2021; 12:1616. [PMID: 34681011 PMCID: PMC8535903 DOI: 10.3390/genes12101616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/20/2021] [Accepted: 10/08/2021] [Indexed: 11/16/2022] Open
Abstract
The evolution of herbicide-resistant weed species is a serious threat for weed control. Therefore, we need an improved understanding of how gene regulation confers herbicide resistance in order to slow the evolution of resistance. The present study analyzed differentially expressed genes after glyphosate treatment on a glyphosate-resistant Tennessee ecotype (TNR) of horseweed (Conyza canadensis), compared to a susceptible biotype (TNS). A read size of 100.2 M was sequenced on the Illumina platform and subjected to de novo assembly, resulting in 77,072 gene-level contigs, of which 32,493 were uniquely annotated by a BlastX alignment of protein sequence similarity. The most differentially expressed genes were enriched in the gene ontology (GO) term of the transmembrane transport protein. In addition, fifteen upregulated genes were identified in TNR after glyphosate treatment but were not detected in TNS. Ten of these upregulated genes were transmembrane transporter or kinase receptor proteins. Therefore, a combination of changes in gene expression among transmembrane receptor and kinase receptor proteins may be important for endowing non-target-site glyphosate-resistant C. canadensis.
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Affiliation(s)
- Yongil Yang
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (Y.Y.); (Y.P.); (C.P.); (R.J.M.)
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Cory Gardner
- Program in Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO 63103, USA; (C.G.); (P.G.); (T.-H.A.)
| | - Pallavi Gupta
- Program in Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO 63103, USA; (C.G.); (P.G.); (T.-H.A.)
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Yanhui Peng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (Y.Y.); (Y.P.); (C.P.); (R.J.M.)
- Centers for Disease Control and Prevention, 1600 Clifton Rd., Atlanta, GA 30333, USA
| | - Cristiano Piasecki
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (Y.Y.); (Y.P.); (C.P.); (R.J.M.)
- ATSI Brasil Pesquisa e Consultoria, Passo Fundo 99054-328, RS, Brazil
| | - Reginald J. Millwood
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (Y.Y.); (Y.P.); (C.P.); (R.J.M.)
| | - Tae-Hyuk Ahn
- Program in Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO 63103, USA; (C.G.); (P.G.); (T.-H.A.)
- Department of Computer Science, Saint Louis University, St. Louis, MO 63103, USA
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (Y.Y.); (Y.P.); (C.P.); (R.J.M.)
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN 37996, USA
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18
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Coates BS, Deleury E, Gassmann AJ, Hibbard BE, Meinke LJ, Miller NJ, Petzold-Maxwell J, French BW, Sappington TW, Siegfried BD, Guillemaud T. Up-regulation of apoptotic- and cell survival-related gene pathways following exposures of western corn rootworm to B. thuringiensis crystalline pesticidal proteins in transgenic maize roots. BMC Genomics 2021; 22:639. [PMID: 34479486 PMCID: PMC8418000 DOI: 10.1186/s12864-021-07932-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/04/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Resistance of pest insect species to insecticides, including B. thuringiensis (Bt) pesticidal proteins expressed by transgenic plants, is a threat to global food security. Despite the western corn rootworm, Diabrotica virgifera virgifera, being a major pest of maize and having populations showing increasing levels of resistance to hybrids expressing Bt pesticidal proteins, the cell mechanisms leading to mortality are not fully understood. RESULTS Twenty unique RNA-seq libraries from the Bt susceptible D. v. virgifera inbred line Ped12, representing all growth stages and a range of different adult and larval exposures, were assembled into a reference transcriptome. Ten-day exposures of Ped12 larvae to transgenic Bt Cry3Bb1 and Gpp34/Tpp35Ab1 maize roots showed significant differential expression of 1055 and 1374 transcripts, respectively, compared to cohorts on non-Bt maize. Among these, 696 were differentially expressed in both Cry3Bb1 and Gpp34/Tpp35Ab1 maize exposures. Differentially-expressed transcripts encoded protein domains putatively involved in detoxification, metabolism, binding, and transport, were, in part, shared among transcripts that changed significantly following exposures to the entomopathogens Heterorhabditis bacteriophora and Metarhizium anisopliae. Differentially expressed transcripts in common between Bt and entomopathogen treatments encode proteins in general stress response pathways, including putative Bt binding receptors from the ATP binding cassette transporter superfamily. Putative caspases, pro- and anti-apoptotic factors, as well as endoplasmic reticulum (ER) stress-response factors were identified among transcripts uniquely up-regulated following exposure to either Bt protein. CONCLUSIONS Our study suggests that the up-regulation of genes involved in ER stress management and apoptotic progression may be important in determining cell fate following exposure of susceptible D. v. virgifera larvae to Bt maize roots. This study provides novel insights into insect response to Bt intoxication, and a possible framework for future investigations of resistance mechanisms.
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Affiliation(s)
- Brad S Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, 103 Genetics Laboratory, Iowa State University, Ames, IA, 50011, USA.
| | | | | | | | - Lance J Meinke
- Department of Entomology, University of Nebraska, Lincoln, NE, USA
| | | | | | - B Wade French
- USDA-ARS, North Central Agricultural Research Laboratory, Brookings, SD, USA
| | - Thomas W Sappington
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, 103 Genetics Laboratory, Iowa State University, Ames, IA, 50011, USA
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Haywood J, Vadlamani G, Stubbs KA, Mylne JS. Antibiotic resistance lessons for the herbicide resistance crisis. PEST MANAGEMENT SCIENCE 2021; 77:3807-3814. [PMID: 33682995 DOI: 10.1002/ps.6357] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 05/26/2023]
Abstract
The challenges of resistance to antibiotics and resistance to herbicides have much in common. Antibiotic resistance became a risk in the 1950s, but a concerted global effort to manage it did not begin until after 2000. Widespread herbicide use began during the 1950s and was soon followed by an unabated rise in resistance. Here, we examine what lessons for combatting herbicide resistance could be learnt from the global, coordinated efforts of all stakeholders to avert the antibiotic resistance crisis. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Joel Haywood
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
| | - Grishma Vadlamani
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Joshua S Mylne
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
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20
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González-Torralva F, Norsworthy JK. Understanding Resistance Mechanisms to Trifluralin in an Arkansas Palmer Amaranth Population. Genes (Basel) 2021; 12:genes12081225. [PMID: 34440399 PMCID: PMC8394034 DOI: 10.3390/genes12081225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/05/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
Amaranthus palmeri S. Watson (Palmer amaranth) is considered a problematic and troublesome weed species in many crops in the USA, partly because of its ability to evolve resistance to herbicides. In this study, we explored the mechanism of resistance in a trifluralin-resistant A. palmeri accession collected from Arkansas, USA. Dose-response assays using agar plates demonstrated an EC50 (effective concentration that reduces root length by 50%) of 1.02 µM trifluralin compared to 0.39 µM obtained in the susceptible accession. Thus, under these conditions, the resistant accession required 2.6 times more trifluralin to inhibit root length by 50%. Seeds in the presence or absence of the cytochrome P450-inhibitior malathion displayed a differential response with no significant influence on root length, suggesting that resistance is not P450-mediated. In addition, application of 4-chloro-7-nitrobenzofurazan (NBD-Cl), a glutathione S-transferase (GST) inhibitor, showed significant differences in root length, indicating that GSTs are most likely involved in the resistance mechanism. Sequencing of α- and β-tubulin genes revealed no single nucleotide polymorphisms (SNPs) previously described between accessions. In addition, relative gene copy number of α- and β-tubulin genes were estimated; however, both resistant and susceptible accessions displayed similar gene copy numbers. Overall, our results revealed that GST-mediated metabolism contributes to trifluralin resistance in this A. palmeri accession from Arkansas.
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Expression stability of internal reference gene in response to Trichoderma polysporum infection in Avena fatua L. Curr Genet 2021; 67:909-918. [PMID: 34287660 DOI: 10.1007/s00294-021-01200-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 10/20/2022]
Abstract
Trichoderma polysporum was a pathogenic fungi which showed strong pathogenicity to Avena fatua L. in recent study. The stress response of A. fatua to T. polysporum is mediated by the regulation of gene expression. Quantification of the expression of genes requires normalizing RT-qPCR data using reference genes with stable expression in the system studied as internal standards. To construct a RT-qPCR system suitable for response of A. fatua to T. polysporum, and screen stable internal reference genes, GeNorm, NormFinder, BestKeeper and RefFinde were used to perform SYBR Green-based RT-qPCR analysis on eight candidate internal reference genes (18S, 28S, TUA, UBC, ACT, GAPDH, TBP and EF-1α) in A. fatua samples after inoculation of T. polysporum Strain HZ-31. The results showed that TBP, 18S and UBC were the most stable internal reference genes, TBP and TUA, TBP and GAPDH, 18S and TBP, UBC and 18S were the most suitable combination of the two internal reference genes, which could be used as internal reference genes for functional gene expression analysis during the interaction between T. polysporum and A. fatua. This is the first study describing a set of reference genes with a stable expression under fungi stress in A. fatua. These genes are also candidate reference genes of choice for studies seeking to identify stress-responsive genes in A. fatua.
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22
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Chen K, Peng Y, Zhang L, Wang L, Mao D, Zhao Z, Bai L, Wang L. Whole transcriptome analysis resulted in the identification of Chinese sprangletop (Leptochloa chinensis) genes involved in cyhalofop-butyl tolerance. BMC Genomics 2021; 22:521. [PMID: 34238252 PMCID: PMC8268407 DOI: 10.1186/s12864-021-07856-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/25/2021] [Indexed: 12/05/2022] Open
Abstract
Background Chinese sprangletop [Leptochloa chinensis (L.) Nees] is an annual malignant weed, which can often be found in paddy fields. Cyhalofop-butyl is a specialized herbicide which is utilized to control L. chinensis. However, in many areas, L. chinensis has become tolerant to this key herbicide due to its continuous long-term use. Results In this study, we utilized a tolerant (LC18002) and a sensitive (LC17041) L. chinensis populations previously identified in our laboratory, which were divided into four different groups. We then employed whole transcriptome analysis to identify candidate genes which may be involved in cyhalofop-butyl tolerance. This analysis resulted in the identification of six possible candidate genes, including three cytochrome P450 genes and three ATP-binding cassette transporter genes. We then carried out a phylogenetic analysis to identify homologs of the differentially expressed cytochrome P450 genes. This phylogenetic analysis indicated that all genes have close homologs in other species, some of which have been implicated in non-target site resistance (NTSR). Conclusions This study is the first to use whole transcriptome analysis to identify herbicide non-target resistance genes in L. chinensis. The differentially expressed genes represent promising targets for better understanding herbicide tolerance in L. chinensis. The six genes belonging to classes already associated in herbicide tolerance may play important roles in the metabolic resistance of L. chinensis to cyhalofop-butyl, although the exact mechanisms require further study. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07856-z.
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Affiliation(s)
- Ke Chen
- Longping Branch, Graduate School of Hunan University, Changsha, People's Republic of China.,Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China.,Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Yajun Peng
- Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Liang Zhang
- Longping Branch, Graduate School of Hunan University, Changsha, People's Republic of China.,Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China.,Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Long Wang
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, 410082, Changsha, People's Republic of China
| | - Donghai Mao
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, 410125, Changsha, People's Republic of China
| | - Zhenghong Zhao
- Longping Branch, Graduate School of Hunan University, Changsha, People's Republic of China
| | - Lianyang Bai
- Longping Branch, Graduate School of Hunan University, Changsha, People's Republic of China. .,Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China. .,Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China.
| | - Lifeng Wang
- Longping Branch, Graduate School of Hunan University, Changsha, People's Republic of China. .,Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China. .,Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China.
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23
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Josephs EB, Van Etten ML, Harkess A, Platts A, Baucom RS. Adaptive and maladaptive expression plasticity underlying herbicide resistance in an agricultural weed. Evol Lett 2021; 5:432-440. [PMID: 34367667 PMCID: PMC8327940 DOI: 10.1002/evl3.241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/29/2021] [Accepted: 05/20/2021] [Indexed: 11/09/2022] Open
Abstract
Plastic phenotypic responses to environmental change are common, yet we lack a clear understanding of the fitness consequences of these plastic responses. Here, we use the evolution of herbicide resistance in the common morning glory (Ipomoea purpurea) as a model for understanding the relative importance of adaptive and maladaptive gene expression responses to herbicide. Specifically, we compare leaf gene expression changes caused by herbicide to the expression changes that evolve in response to artificial selection for herbicide resistance. We identify a number of genes that show plastic and evolved responses to herbicide and find that for the majority of genes with both plastic and evolved responses, plastic responses appear to be adaptive. We also find that selection for herbicide response increases gene expression plasticity. Overall, these results show the importance of adaptive plasticity for herbicide resistance in a common weed and that expression changes in response to strong environmental change can be adaptive. Predicting whether and how organisms will adapt to environmental change is a crucial goal. However, this goal can be complicated because environmental change can alter traits, in a process called plasticity. The extent and fitness consequences of plasticity will have important effects on the adaptive process. In this study, we use adaptation to herbicide in the agricultural weed, the common morning glory, as a model for understanding the extent and fitness consequences of plasticity in gene expression. We find evidence that gene expression plasticity is adaptive in the presence of herbicide, suggesting that understanding plasticity is crucial for understanding how organisms adapt to new environments.
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Affiliation(s)
- Emily B Josephs
- Department of Plant Biology Michigan State University East Lansing Michigan 48824.,Ecology, Evolution, and Behavior Program Michigan State University East Lansing Michigan 48824
| | - Megan L Van Etten
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor Michigan 48109.,Biology Department Pennsylvania State University Dunmore Pennsylvania 18512
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences Auburn University Auburn Alabama 36849.,HudsonAlpha Institute for Biotechnology Huntsville Alabama 35806
| | - Adrian Platts
- Department of Plant Biology Michigan State University East Lansing Michigan 48824
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor Michigan 48109
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24
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Wang L, Wang R, Lei W, Wu J, Li C, Shi H, Meng L, Yuan F, Zhou Q, Cui C. Transcriptome analysis reveals gene responses to herbicide, tribenuron methyl, in Brassica napus L. during seed germination. BMC Genomics 2021; 22:299. [PMID: 33892633 PMCID: PMC8067372 DOI: 10.1186/s12864-021-07614-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/14/2021] [Indexed: 11/25/2022] Open
Abstract
Background Tribenuron methyl (TBM) is an herbicide that inhibits sulfonylurea acetolactate synthase (ALS) and is one of the most widely used broad-leaved herbicides for crop production. However, soil residues or drifting of the herbicide spray might affect the germination and growth of rapeseed, Brassica napus, so it is imperative to understand the response mechanism of rape to TBM during germination. The aim of this study was to use transcriptome analysis to reveal the gene responses in herbicide-tolerant rapeseed to TBM stress during seed germination. Results 2414, 2286, and 1068 differentially expressed genes (DEGs) were identified in TBM-treated resistant vs sensitive lines, treated vs. control sensitive lines, treated vs. control resistant lines, respectively. GO analysis showed that most DEGs were annotated to the oxidation-reduction pathways and catalytic activity. KEGG enrichment was mainly involved in plant-pathogen interactions, α-linolenic acid metabolism, glucosinolate biosynthesis, and phenylpropanoid biosynthesis. Based on GO and KEGG enrichment, a total of 137 target genes were identified, including genes involved in biotransferase activity, response to antioxidant stress and lipid metabolism. Biotransferase genes, CYP450, ABC and GST, detoxify herbicide molecules through physical or biochemical processes. Antioxidant genes, RBOH, WRKY, CDPK, MAPK, CAT, and POD regulate plant tolerance by transmitting ROS signals and triggering antioxidant enzyme expression. Lipid-related genes and hormone-related genes were also found, such as LOX3, ADH1, JAZ6, BIN2 and ERF, and they also played an important role in herbicide resistance. Conclusions This study provides insights for selecting TBM-tolerant rapeseed germplasm and exploring the molecular mechanism of TBM tolerance during germination. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07614-1.
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Affiliation(s)
- Liuyan Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Ruili Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Wei Lei
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Jiayi Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Chenyang Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Hongsong Shi
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Lijiao Meng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Fang Yuan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Qingyuan Zhou
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
| | - Cui Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
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25
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A comparison of shared patterns of differential gene expression and gene ontologies in response to water-stress in roots and leaves of four diverse genotypes of Lolium and Festuca spp. temperate pasture grasses. PLoS One 2021; 16:e0249636. [PMID: 33831050 PMCID: PMC8031407 DOI: 10.1371/journal.pone.0249636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Ryegrasses (Lolium spp.) and fescues (Festuca spp.) are closely related and widely cultivated perennial forage grasses. As such, resilience in the face of abiotic stresses is an important component of their traits. We have compared patterns of differentially expressed genes (DEGs) in roots and leaves of two perennial ryegrass genotypes and a single genotype of each of a festulolium (predominantly Italian ryegrass) and meadow fescue with the onset of water stress, focussing on overall patterns of DEGs and gene ontology terms (GOs) shared by all four genotypes. Plants were established in a growing medium of vermiculite watered with nutrient solution. Leaf and root material were sampled at 35% (saturation) and, as the medium dried, at 15%, 5% and 1% estimated water contents (EWCs) and RNA extracted. Differential gene expression was evaluated comparing the EWC sampling points from RNAseq data using a combination of analysis methods. For all genotypes, the greatest numbers of DEGs were identified in the 35/1 and 5/1 comparisons in both leaves and roots. In total, 566 leaf and 643 root DEGs were common to all 4 genotypes, though a third of these leaf DEGs were not regulated in the same up/down direction in all 4 genotypes. For roots, the equivalent figure was 1% of the DEGs. GO terms shared by all four genotypes were often enriched by both up- and down-regulated DEGs in the leaf, whereas generally, only by either up- or down-regulated DEGs in the root. Overall, up-regulated leaf DEGs tended to be more genotype-specific than down-regulated leaf DEGs or root DEGs and were also associated with fewer GOs. On average, only 5–15% of the DEGs enriching common GO terms were shared by all 4 genotypes, suggesting considerable variation in DEGs between related genotypes in enacting similar biological processes.
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26
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Dixon A, Comont D, Slavov GT, Neve P. Population genomics of selectively neutral genetic structure and herbicide resistance in UK populations of Alopecurus myosuroides. PEST MANAGEMENT SCIENCE 2021; 77:1520-1529. [PMID: 33155426 DOI: 10.1002/ps.6174] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/22/2020] [Accepted: 11/06/2020] [Indexed: 06/07/2023]
Abstract
BACKGROUND Alopecurus myosuroides (blackgrass) is a major weed in Europe with known resistance to multiple herbicide modes of action. In the UK, there is evidence that blackgrass has undergone a range expansion. In this paper, genotyping-by-sequencing and population-level herbicide resistance phenotypes are used to explore spatial patterns of selectively neutral genetic variation and resistance. We also perform a preliminary genome-wide association study (GWAS) and genomic prediction analysis to evaluate the potential of these approaches for investigating nontarget site herbicide resistance. RESULTS Blackgrass was collected from 47 fields across the British Isles and up to eight plants per field population (n = 369) were genotyped by Restriction site-associated DNA (RAD)-sequencing. A total of 20 426 polymorphic loci were identified and used for population genetic analyses. Phenotypic assays revealed significant variation in herbicide resistance between populations. Population structure was weak (FST = 0.024-0.048), but spatial patterns were consistent with an ongoing westward and northward range expansion. We detected strong and consistent Wahlund effects (FIS = 0.30). There were no spatial patterns of herbicide resistance or evidence for confounding with population structure. Using a combination of population-level GWAS and genomic prediction we found that the top 20, 200, and 2000 GWAS loci had higher predictive abilities for fenoxaprop resistance compared to all markers. CONCLUSION There is likely extensive human-mediated gene flow between field populations of the weed blackgrass at a national scale. The lack of confounding of adaptive and neutral genetic variation can enable future, more extensive GWAS analyses to identify the genetic architecture of evolved herbicide resistance. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Andrea Dixon
- Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - David Comont
- Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
| | - Gancho T Slavov
- Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
- Scion, Rotorua, New Zealand
| | - Paul Neve
- Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
- Agriculture & Horticulture Development Board, Warwickshire, UK
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27
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Chen J, Chu Z, Han H, Patterson E, Yu Q, Powles S. Diversity of α-tubulin transcripts in Lolium rigidum. PEST MANAGEMENT SCIENCE 2021; 77:970-977. [PMID: 32991064 DOI: 10.1002/ps.6109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/18/2020] [Accepted: 09/29/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Tubulin, the target site of dinitroaniline herbicides, is encoded by small gene families in plants. To better characterize the mechanisms of target-site resistance to dinitroaniline herbicides in the globally important weedy species Lolium rigidum, attempts were made to amplify and sequence α-tubulin transcripts. RESULTS Four α-tubulin isoforms (TUA1, TUA2, TUA3 and TUA4) were identified in L. rigidum. Variations in the number and sequence of transcripts encoding these α-tubulin proteins were found in individuals from the two L. rigidum populations examined. Within and among populations, differences in the 5'- and 3'-untranslated regions of cDNA in TUA3 and TUA4 were identified. Furthermore, a novel double mutation, Arg-390-Cys+Asp-442-Glu, in the TUA3 transcript was identified and has the potential to confer dinitroaniline resistance. CONCLUSION This research reveals the complexity of the α-tubulin gene family in individuals/populations of the cross-pollinated weedy species L. rigidum, and highlights the need for better understanding of the molecular architecture of tubulin gene families for detecting resistance point mutations. Although TUA4 is a commonly expressed α-tubulin isoform containing most frequently reported resistance mutations, other mutant tubulin isoforms may also have a role in conferring dinitroaniline resistance.
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Affiliation(s)
- Jinyi Chen
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Zhizhan Chu
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Heping Han
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Eric Patterson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Qin Yu
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Stephen Powles
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
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28
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Suzukawa AK, Bobadilla LK, Mallory-Smith C, Brunharo CACG. Non-target-Site Resistance in Lolium spp. Globally: A Review. FRONTIERS IN PLANT SCIENCE 2021; 11:609209. [PMID: 33552102 PMCID: PMC7862324 DOI: 10.3389/fpls.2020.609209] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/07/2020] [Indexed: 05/10/2023]
Abstract
The Lolium genus encompasses many species that colonize a variety of disturbed and non-disturbed environments. Lolium perenne L. spp. perenne, L. perenne L. spp. multiflorum, and L. rigidum are of particular interest to weed scientists because of their ability to thrive in agricultural and non-agricultural areas. Herbicides are the main tool to control these weeds; however, Lolium spp. populations have evolved multiple- and cross-resistance to at least 14 herbicide mechanisms of action in more than 21 countries, with reports of multiple herbicide resistance to at least seven mechanisms of action in a single population. In this review, we summarize what is currently known about non-target-site resistance in Lolium spp. to acetyl CoA carboxylase, acetohydroxyacid synthase, microtubule assembly, photosystem II, 5-enolpyruvylshikimate-3-phosphate synthase, glutamine synthetase, very-long chain fatty acids, and photosystem I inhibitors. We suggest research topics that need to be addressed, as well as strategies to further our knowledge and uncover the mechanisms of non-target-site resistance in Lolium spp.
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Affiliation(s)
- Andréia K. Suzukawa
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - Lucas K. Bobadilla
- Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Carol Mallory-Smith
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - Caio A. C. G. Brunharo
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
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29
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Wang J, Chen J, Li X, Cui H. RNA-Seq transcriptome analysis to identify candidate genes involved in non-target site-based mesosulfuron-methyl resistance in Beckmannia syzigachne. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 171:104738. [PMID: 33357560 DOI: 10.1016/j.pestbp.2020.104738] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/10/2020] [Accepted: 10/21/2020] [Indexed: 06/12/2023]
Abstract
American sloughgrass (Beckmannia syzigachne Steud.) has become a dominant weed in fields with rice-wheat rotation. Moreover, herbicide resistance has rendered weed control difficult. We identified a biotype showing resistance to ALS inhibitor mesosulfuron-methyl with a resistant index 3.3, but without any ALS mutation. This study aims to identify and confirm the factors associated with non-target site resistance of this biotype to mesosulfuron-methyl using RNA-Seq. 118,111 unigenes were assembled, and 50.9% of these were annotated across seven databases. Eleven contigs related to metabolic resistance were identified based on differential expression via RNA-Seq which include a novel resistance-related transcription factor (MYC3) and two disease resistance proteins were also identified (At1g58602 and At1g15890). Fold changes in expression of these genes in comparison M-R vs. M-S ranged from 3.9 to 11.6, as confirmed by qPCR. The expression of a contig annotated as cytochrome P450 (CYP86B1) in resistant individuals was over 3 times higher than that in sensitive individuals at 0-72 h after mesosulfuron-methyl treatment. A similar trend was noted for three other genes annotated as glutathione S-transferase (GST), namely GST-T3, GST-U6, and GST-U14; the expression of GST-U6 in resistant individuals was up to 142.3 times higher than that in sensitive individuals at 24 h after mesosulfuron-methyl treatment. In addition, GST activity in resistant individuals was 2.1 to 5.3 times higher than that in sensitive individuals. The GR50 of resistant biotype decreased from 24.4 to 11.3 g a.i. ha-1 after P450 inhibitor malathion treatment. This study identified a cytochrome P450 gene CYP86B1 and three GST genes GST-T3, GST-U6, and GST-U14 that have higher expression in mesosulfuron-methyl resistant B. syzigachne, suggesting that both P450- and GST-based activities could be involved in resistance.
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Affiliation(s)
- Jingjing Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jingchao Chen
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiangju Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hailan Cui
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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30
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Giacomini DA, Patterson EL, Küpper A, Beffa R, Gaines TA, Tranel PJ. Coexpression Clusters and Allele-Specific Expression in Metabolism-Based Herbicide Resistance. Genome Biol Evol 2020; 12:2267-2278. [PMID: 32915951 PMCID: PMC7738748 DOI: 10.1093/gbe/evaa191] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2020] [Indexed: 01/12/2023] Open
Abstract
In the last decade, Amaranthus tuberculatus has evolved resistance to 2,4-dichlorophenoxyacetic acid (2,4-D) and 4-hydroxyphenylpyruvate dioxygenase inhibitors in multiple states across the midwestern United States. Two populations resistant to both mode-of-action groups, one from Nebraska (NEB) and one from Illinois (CHR), were studied using an RNA-seq approach on F2 mapping populations to identify the genes responsible for resistance. Using both an A. tuberculatus transcriptome assembly and a high-quality grain amaranth (A. hypochondriacus) genome as references, differential transcript and gene expression analyses were conducted to identify genes that were significantly over- or underexpressed in resistant plants. When these differentially expressed genes (DEGs) were mapped on the A. hypochondriacus genome, physical clustering of the DEGs was apparent along several of the 16 A. hypochondriacus scaffolds. Furthermore, single-nucleotide polymorphism calling to look for resistant-specific (R) variants, and subsequent mapping of these variants, also found similar patterns of clustering. Specifically, regions biased toward R alleles overlapped with the DEG clusters. Within one of these clusters, allele-specific expression of cytochrome P450 81E8 was observed for 2,4-D resistance in both the CHR and NEB populations, and phylogenetic analysis indicated a common evolutionary origin of this R allele in the two populations.
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Affiliation(s)
- Darci A Giacomini
- Department of Crop Sciences, University of Illinois Urbana-Champaign
| | - Eric L Patterson
- Department of Plant, Soil and Microbial Sciences, Michigan State University
| | - Anita Küpper
- Bayer AG, Division of Crop Science, Frankfurt, Germany
| | - Roland Beffa
- Bayer AG, Division of Crop Science, Frankfurt, Germany
| | - Todd A Gaines
- Department of Agricultural Biology, Colorado State University
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois Urbana-Champaign
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31
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Bai S, Zhao Y, Zhou Y, Wang M, Li Y, Luo X, Li L. Identification and expression of main genes involved in non-target site resistance mechanisms to fenoxaprop-p-ethyl in Beckmannia syzigachne. PEST MANAGEMENT SCIENCE 2020; 76:2619-2626. [PMID: 32083373 DOI: 10.1002/ps.5800] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/12/2020] [Accepted: 02/21/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Non-target-site resistance (NTSR) to herbicides is a serious threat to global agriculture. Although metabolic resistance is the dominant mechanism of NTSR, the molecular mechanisms are not yet well-characterized. This study aimed to uncover the likely metabolism-related genes in Beckmannia syzigachne (American sloughgrass) resistant to fenoxaprop-p-ethyl. RESULTS Ultra-performance liquid chromatography - tandem mass spectrometry experiments showed that the resistant American sloughgrass biotype (R, SD-04-SS) showed enhanced degradation of this herbicide compared to the susceptible biotype (S, SD-12). R and S biotype were harvested at 24 h after fenoxaprop-p-ethyl treatment to conduct RNA sequencing (RNA-Seq) analysis to investigate the likely fenoxaprop-p-ethyl metabolic genes. The RNA-Seq libraries yield 417 969 980 clean reads. The de novo assembly generated 115 112 unigenes, of which 57 906 unigenes were annotated. Finally, we identified 273 cytochrome P450s, 178 oxidases, 47 glutathione S-transferases (GSTs), 166 glucosyltransferases (GTs) and 180 ABC transporter genes to determine the likely fenoxaprop-p-ethyl metabolism-related genes in R biotype. Twelve overlapping up-regulated genes in the R biotype (fenoxaprop-p-ethyl-treated R/non-treated R, fenoxaprop-p-ethyl-treated R/fenoxaprop-p-ethyl-treated S) were identified by RNA-Seq and the results were validated using qRT-PCR. Ten were identified as fenoxaprop-p-ethyl metabolism-related genes, including three P450s (homologous to CYP71D7, CYP99A2 and CYP71D10), one GST (homologous to GSTF1), two GTs (homologous to UGT90A1 and UGT83A1) and four oxidase genes. CONCLUSION This work demonstrates that the NTSR mechanism by means of enhanced detoxification of fenoxaprop-p-ethyl in American sloughgrass is very likely driven by herbicide metabolism related genes. The RNA-Seq data presented here provide a valuable resource for understanding the molecular mechanism of NTSR in American sloughgrass. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Shuang Bai
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, Qingdao, China
| | - Yanfang Zhao
- College of Chemistry and Pharmacy, Qingdao Agricultural University, Qingdao, China
| | - Yuanming Zhou
- Central Laboratory of Qingdao Agricultural University, Qingdao, China
| | - Mingliang Wang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, Qingdao, China
| | - Yihui Li
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, Qingdao, China
| | - Xiaoyong Luo
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, Qingdao, China
| | - Lingxu Li
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, Qingdao, China
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Li Y, Chen X, Wang J, Zou G, Wang L, Li X. Two responses to MeJA induction of R2R3-MYB transcription factors regulate flavonoid accumulation in Glycyrrhiza uralensis Fisch. PLoS One 2020; 15:e0236565. [PMID: 32730299 PMCID: PMC7392228 DOI: 10.1371/journal.pone.0236565] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/07/2020] [Indexed: 11/19/2022] Open
Abstract
Flavonoids are key components of licorice plant that directly affect its medicinal quality. Importantly, the MYB family of transcription factors serves to regulate the synthesis of flavonoids in plants. The MYB transcription factors represent one of the largest families of transcription factors in plants and play important roles in the process of plant growth and development. MYB gene expression is induced by a number of plant hormones, including the lipid-based hormone jasmonate (JA). Methyl jasmonate (MeJA) is an endogenous plant growth regulator that can induce the JA signaling pathway, which functions to regulate the synthesis of secondary metabolites, including flavonoids. In this study, MeJA was added to licorice cell suspensions, and RNA-seq analysis was performed to identify the differentially expressed genes. As a result, the MYB transcription factors GlMYB4 and GlMYB88 were demonstrated to respond significantly to MeJA induction. Subsequently, the GlMYB4 and GlMYB88 protein were shown to localize to the cell nucleus, and it was verified that GlMYB4 and GlMYB88 could positively regulate the synthesis of flavonoids in licorice cells. Overall, this research helps illustrate the molecular regulation of licorice flavonoid biosynthesis induced by MeJA.
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Affiliation(s)
- Yali Li
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
- * E-mail:
| | - Xiuli Chen
- Baotou Teachers’ College, Biological Science and Technology Institute, Baotou, Inner Mongolia, China
| | - Jiaqi Wang
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Guangping Zou
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Lu Wang
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Xueshuang Li
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
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Gaines TA, Duke SO, Morran S, Rigon CAG, Tranel PJ, Küpper A, Dayan FE. Mechanisms of evolved herbicide resistance. J Biol Chem 2020; 295:10307-10330. [PMID: 32430396 PMCID: PMC7383398 DOI: 10.1074/jbc.rev120.013572] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/18/2020] [Indexed: 12/13/2022] Open
Abstract
The widely successful use of synthetic herbicides over the past 70 years has imposed strong and widespread selection pressure, leading to the evolution of herbicide resistance in hundreds of weed species. Both target-site resistance (TSR) and nontarget-site resistance (NTSR) mechanisms have evolved to most herbicide classes. TSR often involves mutations in genes encoding the protein targets of herbicides, affecting the binding of the herbicide either at or near catalytic domains or in regions affecting access to them. Most of these mutations are nonsynonymous SNPs, but polymorphisms in more than one codon or entire codon deletions have also evolved. Some herbicides bind multiple proteins, making the evolution of TSR mechanisms more difficult. Increased amounts of protein target, by increased gene expression or by gene duplication, are an important, albeit less common, TSR mechanism. NTSR mechanisms include reduced absorption or translocation and increased sequestration or metabolic degradation. The mechanisms that can contribute to NTSR are complex and often involve genes that are members of large gene families. For example, enzymes involved in herbicide metabolism-based resistances include cytochromes P450, GSH S-transferases, glucosyl and other transferases, aryl acylamidase, and others. Both TSR and NTSR mechanisms can combine at the individual level to produce higher resistance levels. The vast array of herbicide-resistance mechanisms for generalist (NTSR) and specialist (TSR and some NTSR) adaptations that have evolved over a few decades illustrate the evolutionary resilience of weed populations to extreme selection pressures. These evolutionary processes drive herbicide and herbicide-resistant crop development and resistance management strategies.
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Affiliation(s)
- Todd A Gaines
- Agricultural Biology Department, Colorado State University, Fort Collins, Colorado, USA
| | - Stephen O Duke
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, Oxford, Mississippi, USA
| | - Sarah Morran
- Agricultural Biology Department, Colorado State University, Fort Collins, Colorado, USA
| | - Carlos A G Rigon
- Agricultural Biology Department, Colorado State University, Fort Collins, Colorado, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Anita Küpper
- Bayer AG, CropScience Division, Frankfurt am Main, Germany
| | - Franck E Dayan
- Agricultural Biology Department, Colorado State University, Fort Collins, Colorado, USA
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Bourdineaud JP. Toxicity of the herbicides used on herbicide-tolerant crops, and societal consequences of their use in France. Drug Chem Toxicol 2020; 45:698-721. [PMID: 32543998 DOI: 10.1080/01480545.2020.1770781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In France, the implementation of mutant herbicide-tolerant crops and the use of the related herbicides - sulfonylureas and imidazolinones - have triggered a strong societal reaction illustrated by the intervening actions of environmentalist groups illegally mowing such crops. Trials are in progress, and therefore should be addressed the questions of the environmental risks and the toxicity of these herbicides for the animals and humans consuming the products derived from these plants. Regulatory authorities have allowed these mutant and herbicide-tolerant plants arguing that the herbicides against which they resist only target an enzyme found in 'weeds' (the acetolactate synthase, ALS), and that therefore all organisms lacking this enzyme would be endowed with immunity to these herbicides. The toxicological literature does not match with this argument: 1) Even in organisms displaying the enzyme ALS, these herbicides impact other molecular targets than ALS; 2) These herbicides are toxic for animals, organisms that do not possess the enzyme ALS, and especially invertebrates, amphibians and fish. In humans, epidemiological studies have shown that the use and handling of these toxins are associated with a significantly increased risk of colon and bladder cancers, and miscarriages. In agricultural soils, these herbicides have a persistence of up to several months, and water samples have concentrations of some of these herbicides above the limit value in drinking water.
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Affiliation(s)
- Jean-Paul Bourdineaud
- Laboratory of Fundamental Microbiology and Pathogenicity, European Institute of Chemistry and Biology, CNRS, University of Bordeaux, Pessac, France.,CRIIGEN, Paris, France
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Transcriptome Analysis Identifies Candidate Target Genes Involved in Glyphosate-Resistance Mechanism in Lolium multiflorum. PLANTS 2020; 9:plants9060685. [PMID: 32481698 PMCID: PMC7357135 DOI: 10.3390/plants9060685] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 05/23/2020] [Accepted: 05/24/2020] [Indexed: 12/23/2022]
Abstract
Italian ryegrass (Lolium multiflorum; LOLMU) is one of the most troublesome weeds in temperate regions in the world. This weed species interfere with wheat, corn, rye, and oat, causing significant crop yield losses. This species has evolved glyphosate resistance, making it difficult to control. The mechanisms of glyphosate resistance are still unknown, and an understanding thereof will favor the development of new strategies of management. The present study is the first transcriptome study in LOLMU using glyphosate-resistant and -sensitive biotypes, aiming to identify and to provide a list of the candidate target genes related to glyphosate resistance mechanism. The transcriptome was assembled de novo, producing 87,433 contigs with an N50 of 740 bp and an average length of 575 bp. There were 92 and 54 up- and down-regulated genes, respectively, in the resistant biotype, while a total of 1683 were differentially expressed in the sensitive biotype in response to glyphosate treatment. We selected 14 highly induced genes and seven with repressed expression in the resistant biotype in response to glyphosate. Of these genes, a significant proportion were related to the plasma membrane, indicating that there is a barrier making it difficult for glyphosate to enter the cell.
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Rai PK, Kim KH, Lee SS, Lee JH. Molecular mechanisms in phytoremediation of environmental contaminants and prospects of engineered transgenic plants/microbes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135858. [PMID: 31846820 DOI: 10.1016/j.scitotenv.2019.135858] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/21/2019] [Accepted: 11/28/2019] [Indexed: 05/06/2023]
Abstract
Concerns about emerging environmental contaminants have been growing along with industrialization and urbanization around the globe. Among various options for remediating these contaminants, phytotechnology is suggested as a feasible option to maintain the environmental sustainability. The recent advances in phytoremediation, genetic/molecular/omics/metabolic engineering, and nanotechnology are opening new paths for efficient treatment of emerging organic/inorganic contaminants. In this respect, elucidation of molecular mechanisms and genetic engineering of hyperaccumulator plants is expected to enhance remediation of environmental contaminants. This review was organized to offer valuable insights into the molecular mechanisms of phytoremediation and the prospects of transgenic hyperaccumulators with enhanced stress tolerance to diverse contaminants such as heavy metals and metalloids, xenobiotics, explosives, poly aromatic hydrocarbons (PAHs), petroleum hydrocarbons, pesticides, and nanoparticles. The roles of genoremediation and nanoparticles in augmenting the phytoremediation technology are also described in an interrelated framework with biotechnological prospects (e.g., plant molecular nano-farming). Finally, political debate on the preferential use of crops versus non-crop hyperaccumulators in genoremediation, limitations of transgenics in phytotechnologies, and their public acceptance issues are discussed in the policy framework.
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Affiliation(s)
- Prabhat Kumar Rai
- Department of Environmental Science, Mizoram University, Aizawl 796004, India
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea.
| | - Sang Soo Lee
- Department of Environmental Engineering, Yonsei University, Wonju 26494, Republic of Korea.
| | - Jin-Hong Lee
- Department of Environmental Engineering, Chungnam National University, Daejeon 34148, Republic of Korea
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Hu Z, Zhang Y, He Y, Cao Q, Zhang T, Lou L, Cai Q. Full-Length Transcriptome Assembly of Italian Ryegrass Root Integrated with RNA-Seq to Identify Genes in Response to Plant Cadmium Stress. Int J Mol Sci 2020; 21:ijms21031067. [PMID: 32041113 PMCID: PMC7037684 DOI: 10.3390/ijms21031067] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/02/2020] [Accepted: 02/04/2020] [Indexed: 12/13/2022] Open
Abstract
Cadmium (Cd) is a toxic heavy metal element. It is relatively easily absorbed by plants and enters the food chain, resulting in human exposure to Cd. Italian ryegrass (Lolium multiflorum Lam.), an important forage cultivated widely in temperate regions worldwide, has the potential to be used in phytoremediation. However, genes regulating Cd translocation and accumulation in this species are not fully understood. Here, we optimized PacBio ISO-seq and integrated it with RNA-seq to construct a de novo full-length transcriptomic database for an un-sequenced autotetraploid species. With the database, we identified 2367 differentially expressed genes (DEGs) and profiled the molecular regulatory pathways of Italian ryegrass with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis in response to Cd stress. Overexpression of a DEG LmAUX1 in Arabidopsis thaliana significantly enhanced plant Cd concentration. We also unveiled the complexity of alternative splicing (AS) with a genome-free strategy. We reconstructed full-length UniTransModels using the reference transcriptome, and 29.76% of full-length models had more than one isoform. Taken together, the results enhanced our understanding of the genetic diversity and complexity of Italian ryegrass under Cd stress and provided valuable genetic resources for its gene identification and molecular breeding.
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Perotti VE, Larran AS, Palmieri VE, Martinatto AK, Permingeat HR. Herbicide resistant weeds: A call to integrate conventional agricultural practices, molecular biology knowledge and new technologies. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110255. [PMID: 31779903 DOI: 10.1016/j.plantsci.2019.110255] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 05/16/2023]
Abstract
Herbicide resistant (HR) weeds are of major concern in modern agriculture. This situation is exacerbated by the massive adoption of herbicide-based technologies along with the overuse of a few active ingredients to control weeds over vast areas year after year. Also, many other anthropological, biological, and environmental factors have defined a higher rate of herbicide resistance evolution in numerous weed species around the world. This review focuses on two central points: 1) how these factors have affected the resistance evolution process; and 2) which cultural practices and new approaches would help to achieve an effective integrated weed management. We claim that global climate change is an unnoticed factor that may be acting on the selection of HR weeds, especially those evolving into non-target-site resistance mechanisms. And we present several new tools -such as Gene Drive and RNAi technologies- that may be adopted to cope with herbicide resistance spread, as well as discuss their potential application at field level. This is the first review that integrates agronomic and molecular knowledge of herbicide resistance. It covers not only the genetic basis of the most relevant resistance mechanisms but also the strengths and weaknesses of traditional and forthcoming agricultural practices.
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Affiliation(s)
- Valeria E Perotti
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina
| | - Alvaro S Larran
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina; Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina
| | - Valeria E Palmieri
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina
| | - Andrea K Martinatto
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina
| | - Hugo R Permingeat
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina; Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina.
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Omics Potential in Herbicide-Resistant Weed Management. PLANTS 2019; 8:plants8120607. [PMID: 31847327 PMCID: PMC6963460 DOI: 10.3390/plants8120607] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 12/20/2022]
Abstract
The rapid development of omics technologies has drastically altered the way biologists conduct research. Basic plant biology and genomics have incorporated these technologies, while some challenges remain for use in applied biology. Weed science, on the whole, is still learning how to integrate omics technologies into the discipline; however, omics techniques are more frequently being implemented in new and creative ways to address basic questions in weed biology as well as the more practical questions of improving weed management. This has been especially true in the subdiscipline of herbicide resistance where important questions are the evolution and genetic basis of herbicide resistance. This review examines the advantages, challenges, potential solutions, and outlook for omics technologies in the discipline of weed science, with examples of how omics technologies will impact herbicide resistance studies and ultimately improve management of herbicide-resistant populations.
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Zhao N, Ge L, Yan Y, Bai S, Wang D, Liu W, Wang J. Trp-1999-Ser mutation of acetyl-CoA carboxylase and cytochrome P450s-involved metabolism confer resistance to fenoxaprop-P-ethyl in Polypogon fugax. PEST MANAGEMENT SCIENCE 2019; 75:3175-3183. [PMID: 30950550 DOI: 10.1002/ps.5435] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Asia minor bluegrass (Polypogon fugax Nees ex Steud.) is an invasive grass species severely infesting wheat and canola fields in China. In May 2017, a suspected resistant P. fugax population AHHY that survived fenoxaprop-P-ethyl applied at its field-recommended rate was collected from a wheat field in Huaiyuan County, Anhui Province, China. This study aimed to determine the resistance profile of AHHY to acetyl-CoA carboxylase (ACCase) inhibitors and to investigate its mechanisms of resistance to fenoxaprop. RESULTS Single-dose testing indicated that the AHHY population had evolved resistance to fenoxaprop. The partial carboxyltransferase domain of ACCase in P. fugax was amplified and compared. Four loci encoding plastidic ACCase were isolated from both the resistant and sensitive individuals. Combining gene sequencing with the derived cleaved amplified polymorphic sequence assay, we found that 100% of the plants of AHHY carried Trp-1999-Ser mutation in their ACCase1,1-2 allele. Whole-plant dose-response bioassay indicated that AHHY was highly resistant to fenoxaprop and pinoxaden (resistance index (RI) ≥ 10) with low resistance to clodinafop-propargyl, sethoxydim, and clethodim (2 ≤ RI < 5). Pre-treatment with piperonyl butoxide largely reduced (55%) the weed's resistance to fenoxaprop. Both basal and fenoxaprop-induced glutathione S-transferases activities toward 1-chloro-2, 4-dinitrobenzene were significantly higher in resistant plants than in susceptible plants. CONCLUSION This study revealed that P. fugax had multiple alleles encoding plastidic ACCase, and reported for the first time the occurrence of Trp-1999-Ser mutation and non-target-site resistance in this species. Fenoxaprop resistance in AHHY plants was conferred by target-site mutation and P450s-involved enhanced metabolism. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Ning Zhao
- College of Plant Protection, Shandong Agricultural University, Tai'an, China
- Key Laboratory of Pesticide Toxicology and Application Technology, Shandong Agricultural University, Tai'an, China
| | - Lu'an Ge
- College of Plant Protection, Shandong Agricultural University, Tai'an, China
- Key Laboratory of Pesticide Toxicology and Application Technology, Shandong Agricultural University, Tai'an, China
| | - Yanyan Yan
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Shuang Bai
- College of Plant Protection, Shandong Agricultural University, Tai'an, China
- Key Laboratory of Pesticide Toxicology and Application Technology, Shandong Agricultural University, Tai'an, China
| | - Dandan Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an, China
- Key Laboratory of Pesticide Toxicology and Application Technology, Shandong Agricultural University, Tai'an, China
| | - Weitang Liu
- College of Plant Protection, Shandong Agricultural University, Tai'an, China
- Key Laboratory of Pesticide Toxicology and Application Technology, Shandong Agricultural University, Tai'an, China
| | - Jinxin Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an, China
- Key Laboratory of Pesticide Toxicology and Application Technology, Shandong Agricultural University, Tai'an, China
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Non-Target-Site Resistance to Herbicides: Recent Developments. PLANTS 2019; 8:plants8100417. [PMID: 31618956 PMCID: PMC6843234 DOI: 10.3390/plants8100417] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/10/2019] [Accepted: 10/12/2019] [Indexed: 01/07/2023]
Abstract
Non-target-site resistance (NTSR) to herbicides in weeds can be conferred as a result of the alteration of one or more physiological processes, including herbicide absorption, translocation, sequestration, and metabolism. The mechanisms of NTSR are generally more complex to decipher than target-site resistance (TSR) and can impart cross-resistance to herbicides with different modes of action. Metabolism-based NTSR has been reported in many agriculturally important weeds, although reduced translocation and sequestration of herbicides has also been found in some weeds. This review focuses on summarizing the recent advances in our understanding of the physiological, biochemical, and molecular basis of NTSR mechanisms found in weed species. Further, the importance of examining the co-existence of TSR and NTSR for the same herbicide in the same weed species and influence of environmental conditions in the altering and selection of NTSR is also discussed. Knowledge of the prevalence of NTSR mechanisms and co-existing TSR and NTSR in weeds is crucial for designing sustainable weed management strategies to discourage the further evolution and selection of herbicide resistance in weeds.
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Fang J, Zhang Y, Liu T, Yan B, Li J, Dong L. Target-Site and Metabolic Resistance Mechanisms to Penoxsulam in Barnyardgrass ( Echinochloa crus-galli (L.) P. Beauv). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:8085-8095. [PMID: 31265279 DOI: 10.1021/acs.jafc.9b01641] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Herbicide resistance identification is essential for effective chemical weed control. In this study, we quantified the differences in growth response between penoxsulam resistant (R) and sensitive (S) Echinochloa crus-galli populations, explored the changes in ALS, and performed genetic analyses to identify metabolic genes that are up-regulated by the application of penoxsulam and other common herbicides. The R population showed a 26.0-fold higher resistance to penoxsulam and varied resistance to most tested herbicides with indices ranging from 4.9 to 145.9. A Trp-574-Arg amino acid mutation in ALS and low penoxsulam ALS sensitivity were the main mechanisms underlying herbicide resistance. The penoxsulam resistance can be significantly reversed by two P450s inhibitors and one GST inhibitor. By RNA-Seq, thirty-six highly expressed contigs were selected, and 30 of them were up-regulated in the R population treated by penoxsulam. Many of these genes were significantly expressed when treated with pyroxsulam, metamifop, and quinclorac. These upregulated genes appear to be complementary for plant resistance to penoxsulam and other common herbicides.
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Affiliation(s)
- Jiapeng Fang
- College of Plant Protection , Nanjing Agricultural University , Nanjing 210095 , People's Republic of China
- State and Local Joint Engineering Research Center of Green Pesticide Invention and Application , Nanjing 210095 , People's Republic of China
| | - Yuhua Zhang
- College of Plant Protection , Nanjing Agricultural University , Nanjing 210095 , People's Republic of China
- State and Local Joint Engineering Research Center of Green Pesticide Invention and Application , Nanjing 210095 , People's Republic of China
| | - Tingting Liu
- College of Plant Protection , Nanjing Agricultural University , Nanjing 210095 , People's Republic of China
- State and Local Joint Engineering Research Center of Green Pesticide Invention and Application , Nanjing 210095 , People's Republic of China
| | - Bojun Yan
- College of Plant Protection , Nanjing Agricultural University , Nanjing 210095 , People's Republic of China
- State and Local Joint Engineering Research Center of Green Pesticide Invention and Application , Nanjing 210095 , People's Republic of China
| | - Jun Li
- College of Plant Protection , Nanjing Agricultural University , Nanjing 210095 , People's Republic of China
- State and Local Joint Engineering Research Center of Green Pesticide Invention and Application , Nanjing 210095 , People's Republic of China
| | - Liyao Dong
- College of Plant Protection , Nanjing Agricultural University , Nanjing 210095 , People's Republic of China
- State and Local Joint Engineering Research Center of Green Pesticide Invention and Application , Nanjing 210095 , People's Republic of China
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Lian JL, Ren LS, Zhang C, Yu CY, Huang Z, Xu AX, Dong JG. How exposure to ALS-inhibiting gametocide tribenuron-methyl induces male sterility in rapeseed. BMC PLANT BIOLOGY 2019; 19:124. [PMID: 30940071 PMCID: PMC6444545 DOI: 10.1186/s12870-019-1722-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 03/17/2019] [Indexed: 06/08/2023]
Abstract
BACKGROUND Acetolactate synthase (ALS)-inhibiting herbicide tribenuron-methyl (TBM) is an efficient gametocide that can cause rapeseed (Brassica napus L.) to become male sterile and outcrossing. To find the reason the TBM treatment leads to male sterility, an integrated study using cytological, physiological, and transcriptomic methods was conducted. RESULTS Some temporary symptoms, including the discoloration of young leaves and a short halt of raceme elongation, were observed in the rapeseed plants exposed to TBM at an application rate of 1 μg per plant. Both chloroplasts in young leaves and plastids in anthers were deformed. TBM also reduced the leaf photosynthetic rate and the contents of chlorophyll, soluble sugar and pyruvate. Both the tapetal cells and uni-nucleate microspores in the treated plants showed large autophagic vacuoles, and the tissue degenerated quickly. A transcriptomic comparison with the control identified 200 upregulated and 163 downregulated differential expression genes in the small flower buds of the TBM treatment. The genes encoding functionally important proteins, including glucan endo-1,3-beta-glucosidase A6, QUARTET3 (QRT3), ARABIDOPSIS ANTHER 7 (ATA7), non-specific lipid-transfer protein LTP11 and LTP12, histone-lysine N-methyltransferase ATXR6, spermidine coumaroyl-CoA acyltransferase (SCT), and photosystem II reaction centre protein psbB, were downregulated by TBM exposure. Some important genes encoding autophagy-related protein ATG8a and metabolic detoxification related proteins, including DTX1, DTX6, DTX35, cytosolic sulfotransferase SOT12, and six members of glutathione S-transferase, were upregulated. In addition, several genes related to hormone stimulus, such as 1-aminocyclopropane-1-carboxylate synthase 8 (ACS8), ethylene-responsive factor ERF1A, ERF1, ERF71, CRF6, and RAP2-3, were also upregulated. The transcriptional regulation is in accordance with the functional abnormalities of pollen wall formation, lipid metabolism, chloroplast structure, ethylene generation, cell cycle, and tissue autophagy. CONCLUSION The results suggested that except for ALS, the metabolic pathways related to lipid metabolism, pollen exine formation, photosynthesis and hormone response are associated with male sterility induced by TBM. The results provide new insight into the molecular mechanisms of inducing male sterility by sulfonylurea.
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Affiliation(s)
- Jing-long Lian
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Li-Suo Ren
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Cong Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Cheng-Yu Yu
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Zhen Huang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Ai-Xia Xu
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jun-Gang Dong
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
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Bai S, Zhang F, Li Z, Wang H, Wang Q, Wang J, Liu W, Bai L. Target-site and non-target-site-based resistance to tribenuron-methyl in multiply-resistant Myosoton aquaticum L. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 155:8-14. [PMID: 30857630 DOI: 10.1016/j.pestbp.2018.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/06/2018] [Accepted: 12/13/2018] [Indexed: 06/09/2023]
Abstract
Myosoton aquaticum L., a widespread and competitive winter weed of wheat in China, has evolved resistance to many classes of herbicides. In one M. aquaticum population (AH03), collected from Anhui Province, where tribenuron-methyl and florasulam had been used to control this weed resistance to both herbicides had evolved. Compared with the sensitive population, HN03(S), the resistant (R) population, AH03, was highly resistant to tribenuron-methyl, flucarbazone-Na and pyroxsulam, moderately resistant to pyrithiobac‑sodium, and florasulam, and had low resistance to diflufenican. AH03 was still controlled by imazethapyr, 2,4-D butylate, fluroxypyr-meptyl, and isoproturon. Pretreatment with the P450 inhibitor malathion reduced the GR50 value of tribenuron-methyl by 43% in the R population, and by 25% in the S population. This indicates that P450-mediated enhanced metabolism is one likely mechanism for tribenuron-methyl resistance in M. aquaticum. Glutathione-S-transferase (GST) activity could be induced by tribenuron-methyl in both the R and S populations. However, both the basal and induced GST activity of the R population was lower than that of the S population. The in vitro ALS assay confirmed that the ALS from the R plants showed a high resistance (52.93-fold) to tribenuron-methyl. ALS gene sequencing revealed a Pro197Ala substitution in the R plants. Based on the ALS gene sequence analysis, molecular markers were also developed to identify the specific Pro197Ala mutation. This population of M. aquaticum has multiple resistance and target-site (ALS Pro197Ala) and non-target-site resistance mechanisms contribute to tribenuron-methyl resistance.
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Affiliation(s)
- Shuang Bai
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China; Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Fengwen Zhang
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China; Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Zuren Li
- Hunan Provincial Key Laboratory for Biology and Control of Weed, Changsha, Hunan 410125, China
| | - Hengzhi Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China; Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Qian Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China; Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Jinxin Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China; Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Weitang Liu
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China; Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China.
| | - Lianyang Bai
- Hunan Provincial Key Laboratory for Biology and Control of Weed, Changsha, Hunan 410125, China.
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Oliveira MC, Gaines TA, Patterson EL, Jhala AJ, Irmak S, Amundsen K, Knezevic SZ. Interspecific and intraspecific transference of metabolism-based mesotrione resistance in dioecious weedy Amaranthus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:1051-1063. [PMID: 30218635 DOI: 10.1111/tpj.14089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/01/2018] [Accepted: 09/06/2018] [Indexed: 06/08/2023]
Abstract
Pollen-mediated gene flow (PMGF) might play an important role in dispersing herbicide resistance alleles in dioecious weedy Amaranthus species. Field experiments in a concentric donor-receptor design were conducted to quantify two sets of PMGF studies, an interspecific (Amaranthus tuberculatus × Amaranthus palmeri) and an intraspecific (A. tuberculatus × A. tuberculatus). In both studies, PMGF was evaluated using a resistant A. tuberculatus phenotype with enhanced mesotrione detoxification via P450 enzymes as a source of resistance alleles. For interspecific hybridization, more than 104 000 putative hybrid seedlings were screened with three markers, one phenotypic and two molecular. The two molecular markers used, including 2-bp polymorphisms in the internal transcribed spacer region, distinguished A. palmeri, A. tuberculatus and their hybrids. Results showed that 0.1% hybridization between A. tuberculatus × A. palmeri occurred under field research conditions. For intraspecific hybridization, 22 582 seedlings were screened to assess the frequency of gene flow. The frequency of gene flow (FGF ) varied with distance, direction and year of the study. The farthest distance for 90% reduction of FGF was at 69 m in 2015 however, after averaging across directions it was 13.1 and 26.1 m in 2014 and 2015, respectively. This study highlights the transfer of metabolism-based mesotrione resistance from A. tuberculatus to A. palmeri under field research conditions. The results presented here might aid in the rapid detection of A. palmeri among other Amaranthus species and show that PMFG could be expediting the increase of herbicide resistance in A. palmeri and A. tuberculatus across US crop production areas.
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Affiliation(s)
- Maxwel C Oliveira
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Todd A Gaines
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Eric L Patterson
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Amit J Jhala
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Suat Irmak
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Keenan Amundsen
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Stevan Z Knezevic
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
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Liu W, Bai S, Zhao N, Jia S, Li W, Zhang L, Wang J. Non-target site-based resistance to tribenuron-methyl and essential involved genes in Myosoton aquaticum (L.). BMC PLANT BIOLOGY 2018; 18:225. [PMID: 30305027 PMCID: PMC6180388 DOI: 10.1186/s12870-018-1451-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 09/27/2018] [Indexed: 05/30/2023]
Abstract
BACKGROUND Water chickweed (Myosoton aquaticum (L.)) is a dicot broadleaf weed that is widespread in winter fields in China, and has evolved serious resistance to acetolactate synthase (ALS) inhibiting herbicides. RESULTS We identified a M. aquaticum population exhibiting moderate (6.15-fold) resistance to tribenuron-methyl (TM). Target-site ALS gene sequencing revealed no known resistance mutations in these plants, and the in vitro ALS activity assays showed no differences in enzyme sensitivity between susceptible and resistant populations; however, resistance was reversed by pretreatment with the cytochrome P450 (CYP) monooxygenase inhibitor malathion. An RNA sequencing transcriptome analysis was performed to identify candidate genes involved in metabolic resistance, and the unigenes obtained by de novo transcriptome assembly were annotated across seven databases. In total, 34 differentially expressed genes selected by digital gene expression analysis were validated by quantitative real-time (qRT)-PCR. Ten consistently overexpressed contigs, including four for CYP, four for ATP-binding cassette (ABC) transporter, and two for peroxidase were further validated by qRT-PCR using additional plants from resistant and susceptible populations. Three CYP genes (with homology to CYP734A1, CYP76C1, and CYP86B1) and one ABC transporter gene (with homology to ABCC10) were highly expressed in all resistant plants. CONCLUSION The mechanism of TM resistance in M. aquaticum is controlled by NTSR rather than TSR. Four genes, CYP734A1, CYP76C1, CYP86B1, and ABCC10 could play essential role in metabolic resistance to TM and justify further functional studies. To our knowledge, this is the first large-scale transcriptome analysis of genes associated with NTSR in M. aquaticum using the Illumina platform. Our data provide resource for M. aquaticum biology, and will facilitate the study of herbicide resistance mechanism at the molecular level in this species as well as in other weeds.
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Affiliation(s)
- Weitang Liu
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Taian, 271018 Shandong China
| | - Shuang Bai
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Taian, 271018 Shandong China
| | - Ning Zhao
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Taian, 271018 Shandong China
| | - Sisi Jia
- Taian Customs, Taian, 271000 Shandong China
| | - Wei Li
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Taian, 271018 Shandong China
| | - Lele Zhang
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Taian, 271018 Shandong China
| | - Jinxin Wang
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Taian, 271018 Shandong China
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Giacomini DA, Gaines T, Beffa R, Tranel PJ. Optimizing RNA-seq studies to investigate herbicide resistance. PEST MANAGEMENT SCIENCE 2018; 74:2260-2264. [PMID: 29222921 DOI: 10.1002/ps.4822] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 11/21/2017] [Accepted: 12/01/2017] [Indexed: 05/11/2023]
Abstract
Transcriptomic profiling, specifically via RNA sequencing (RNA-seq), is becoming one of the more commonly used methods for investigating non-target site resistance (NTSR) to herbicides due to its high throughput capabilities and utility in organisms with little to no previous sequence information. A review of the weed science RNA-seq literature revealed some basic principles behind generating quality data from these types of studies. First, studies that included more replicates per biotype and took steps to control for genetic background had significantly better control of false positives and, consequently, shorter lists of potential resistance genes to sift through. Pooling of biological replicates prior to sequencing was successful in some cases, but likely contributed to an overall increase in the false discovery rate. Although the inclusion of herbicide-treated samples was common across most of the studies, it ultimately introduced difficulties in interpretation of the final results due to challenges in capturing the right sampling window after treatment and to the induction of stress responses in the injured herbicide-sensitive plants. RNA-seq is an effective tool for NTSR gene discovery, but careful consideration should be given to finding the most powerful and cost-effective balance between replicate number, sequencing depth and treatment number. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Darci A Giacomini
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Todd Gaines
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Roland Beffa
- Bayer AG, CropScience Division, Industriepark Hoechst, Frankfurt, Germany
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
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Goggin DE, Kaur P, Owen MJ, Powles SB. 2,4-D and dicamba resistance mechanisms in wild radish: subtle, complex and population specific? ANNALS OF BOTANY 2018; 122:627-640. [PMID: 29893784 PMCID: PMC6153477 DOI: 10.1093/aob/mcy097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 05/11/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Resistance to synthetic auxin herbicides such as 2,4-dichlorophenoxyacetic acid (2,4-D) is increasing in weed populations worldwide, which is of concern given the recent introduction of synthetic auxin-resistant transgenic crops. Due to the complex mode of action of the auxinic herbicides, the mechanisms of evolved resistance remain largely uncharacterized. The aims of this study were to assess the level of diversity in resistance mechanisms in 11 populations of the problem weed Raphanus raphanistrum, and to use a high-throughput, whole-genome transcriptomic analysis on one resistant and one susceptible population to identify important changes in gene expression in response to 2,4-D. METHODS Levels of 2,4-D and dicamba (3,6-dichloro-2-methoxybenzoic acid) resistance were quantified in a dose-response study and the populations were further screened for auxin selectivity, 2,4-D translocation and metabolism, expression of key 2,4-D-responsive genes and activation of the mitogen-activated proein kinase (MAPK) pathway. Potential links between resistance levels and mechanisms were assessed using correlation analysis. KEY RESULTS The transcriptomic study revealed early deployment of the plant defence response in the 2,4-D-treated resistant population, and there was a corresponding positive relationship between auxinic herbicide resistance and constitutive MAPK phosphorylation across all populations. Populations with shoot-wide translocation of 2,4-D had similar resistance levels to those with restricted translocation, suggesting that reduced translocation may not be as strong a resistance mechanism as originally thought. Differences in auxin selectivity between populations point to the likelihood of different resistance-conferring alterations in auxin signalling and/or perception in the different populations. CONCLUSIONS 2,4-D resistance in wild radish appears to result from subtly different auxin signalling alterations in different populations, supplemented by an enhanced defence response and, in some cases, reduced 2,4-D translocation. This study highlights the dangers of applying knowledge generated from a few populations of a weed species to the species as a whole.
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Affiliation(s)
- Danica E Goggin
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, The University of Western Australia, Crawley, Australia
- For correspondence. E-mail
| | - Parwinder Kaur
- Centre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Crawley, Australia
- Institute of Agriculture, The University of Western Australia, Crawley, Australia
- Telethon Kids Institute, Subiaco, Australia
| | - Mechelle J Owen
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, The University of Western Australia, Crawley, Australia
| | - Stephen B Powles
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, The University of Western Australia, Crawley, Australia
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Bai S, Liu W, Wang H, Zhao N, Jia S, Zou N, Guo W, Wang J. Enhanced Herbicide Metabolism and Metabolic Resistance Genes Identified in Tribenuron-Methyl Resistant Myosoton aquaticum L. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:9850-9857. [PMID: 30142979 DOI: 10.1021/acs.jafc.8b02740] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The evolved resistance of Myosoton aquaticum L. to acetolactate synthase (ALS) inhibitors is well established, but most research has focused on target-site resistance, while nontarget-site resistance remains neglected. Here, we investigated mechanisms of the latter. The pretreatment with the P450 inhibitor malathion significantly increased the sensitivity of resistant plants to tribenuron-methyl. The rapid P450-mediated tribenuron-methyl metabolism in resistant plants was confirmed by LC-MS/MS analysis. Besides, GST activity was higher among resistant than susceptible individuals. The next transcriptome analysis generated 544,102,236 clean reads from RNA sequencing libraries. De novo assembly yielded 102,529 unigenes with an average length of 866 bp, annotated across seven databases. Digital gene expression selected 25 differentially expressed genes, further validated with qRT-PCR. Three P450 genes, two GST genes, two glucosyltransferase genes, four ABC transporter genes, and four additional contigs were constitutively up-regulated in resistant individuals. Overall, our research confirmed that enhanced herbicide metabolism drives tribenuron-methyl resistance in M. aquaticum.
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Affiliation(s)
- Shuang Bai
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
| | - Weitang Liu
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
| | - Hengzhi Wang
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
| | - Ning Zhao
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
| | - Sisi Jia
- Taian Customs , Tai'an 271000 , Shandong , China
| | - Nan Zou
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
| | - Wenlei Guo
- Plant Protection Research Institute , Guangdong Academy of Agricultural Sciences , Guangzhou 510640 , P.R. China
| | - Jinxin Wang
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection , Shandong Agricultural University , Tai'an 271018 , Shandong , China
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Yang L, Xu Y, Zhang R, Wang X, Yang C. Comprehensive transcriptome profiling of soybean leaves in response to simulated acid rain. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 158:18-27. [PMID: 29656160 DOI: 10.1016/j.ecoenv.2018.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
As a source of edible oil and protein, soybean is a major globally important economic crop; Improving its production has been an important objective of soybean breeding. Acid rain has been shown to influence soybean growth and productivity, with consequent adverse impacts on its production for use by human populations. In this study, RNA sequencing technology was utilized to examine changes in gene expression when soybean was exposed to simulated acid rain (SAR). We sampled soybean leaves at five time intervals (0, 6, 30, 54, 78, and 102 h), and built the cDNA library. In total, 54,175 expression genes were found, including 2016 genes with differential expression. A total of 416 genes were considered, as they were closely related to the response to SAR. Genes related to the regulation of sulfur and nitrogen metabolism, carbohydrate metabolism, photosynthesis, and reactive oxygen species were among those differentially expressed in response to SAR. In this study, we examined the response mechanisms of soybean under SAR exposure. Our findings will improve our understanding of the molecular mechanisms employed by soybean in responding to abiotic stress, and therefore provides important information in developing soybean breeding to improve tolerance to these stresses.
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Affiliation(s)
- Long Yang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Yongchao Xu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Rui Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Xiaotong Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Chao Yang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China.
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