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Kaundun SS, Martin-Sanz A, Rodríguez M, Serbanoiu T, Moreno J, Mcindoe E, le Goupil G. First case of evolved herbicide resistance in the holoparasite sunflower broomrape, Orobanche cumana Wallr. FRONTIERS IN PLANT SCIENCE 2024; 15:1420009. [PMID: 38895610 PMCID: PMC11184133 DOI: 10.3389/fpls.2024.1420009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024]
Abstract
The development and commercialisation of sunflower varieties tolerant to acetolactate synthase (ALS)-inhibiting herbicides some 20 years ago provided farmers with an alternative method for the cost-effective control of Orobanche cumana. In 2020, however, two independent sunflower broomrape populations from Drama (GR-DRA) and Orestiada (GR-ORE), Greece, were reported to be heavily infested with O. cumana after application of the ALS-inhibiting herbicide imazamox. Here we have investigated the race of GR-DRA and GR-ORE and determined the basis of resistance to imazamox in the two Greek O. cumana samples. Using a set of five diagnostic sunflower varieties characterised by different resistant genes with respect to O. cumana infestation, we have clearly established that the GR-ORE and GR-DRA populations belong to the invasive broomrape races G and G+, respectively. Live underground tubercles and emerged shoots were identified at the recommended field rate of imazamox for GR-DRA and GR-ORE but not for two other standard sensitive populations in a whole plant dose response test using two different herbicide-tolerant sunflower hybrids as hosts. Sequencing of the ALS gene identified an alanine 205 to aspartate mutation in all GR-ORE samples. Most GR-DRA tubercles were characterised by a second serine 653 to asparagine ALS mutation whilst a few GR-DRA individuals contained the A205D mutation. Mutations at ALS codons 205 and 653 are known to impact on the binding and efficacy of imazamox and other imidazolinone herbicides. The knowledge generated here will be important for tracking and managing broomrape resistance to ALS-inhibiting herbicides in sunflower growing regions.
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Affiliation(s)
- Shiv Shankhar Kaundun
- Syngenta Ltd, Jealott’s Hill International Research Centre, Bracknell, Berkshire, United Kingdom
| | | | | | | | - Jose Moreno
- Syngenta Ltd, Jealott’s Hill International Research Centre, Bracknell, Berkshire, United Kingdom
| | - Eddie Mcindoe
- Syngenta Ltd, Jealott’s Hill International Research Centre, Bracknell, Berkshire, United Kingdom
| | - Gael le Goupil
- Syngenta Crop Protection AG, Werk Rosental, Basel, Switzerland
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Unan R, Azapoglu O, Deligoz İ, Mennan H, Al-Khatib K. Gene flow and spontaneous mutations are responsible for imidazolinone herbicide-resistant weedy rice (Oryza sativa L.). PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 198:105746. [PMID: 38225089 DOI: 10.1016/j.pestbp.2023.105746] [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: 11/16/2023] [Revised: 12/07/2023] [Accepted: 12/10/2023] [Indexed: 01/17/2024]
Abstract
For more than two decades, weedy rice (Oryza sativa L.) has been controlled in rice fields by using imidazolinone (IMI) herbicide-resistant rice technology (Clearfield®). Outcrossing in weedy rice populations and spontaneous mutations are potential problems with herbicide-resistant crop management technologies, such as the IMI-resistant rice. The aim of this study was to characterize the mechanism of IMI herbicide resistance in weedy rice through dose-response bioassay study and evaluating amino acid substitutions in acetolactate synthase (ALS) protein. A total of 118 suspected IMI-resistant weedy rice samples, which survived in the field after an IMI herbicide application, were collected at harvest time from Türkiye in 2020 and 2021. Single-dose imazamox application experiment revealed that 38 plants survived herbicide treatment. The imazamox resistance of the surviving plants was confirmed by dose-response experiment. ALS gene region underwent a sanger DNA partial sequencing. No substitution was found in 10 samples, however, amino acid substitutions were found in 26 samples with S563N, one sample with S653T, and one sample with E630D. The S653N point is the same substitution point that serves as the origin of resistance for the Clearfield® rice varieties that are commonly cultivated in the region. It has been hypothesized that the gene flow from IMI-resistant rice may be the cause of resistance in the IMI resistant weedy rice samples with S653N. The other substitution, S653T, were considered spontaneous mutation to IMI resistance. Interestingly, the S653T mutation was detected for the first time in weedy rice. The mechanism of resistance of 10 resistant weedy rice was not confirmed in this study, however, it may be a non-target resistance or another mutation point in target site, but evidently, they did not acquire resistance by gene flow from IMI-resistant rice. It has been concluded that the effectiveness of IMI-resistant rice technology in controlling weedy rice has drastically decreased due to possible gene flow, spontaneous mutation and non-target resistance. In addition to cultural controls like clean seed, clean machinery and crop rotation, other herbicide-tolerant rice systems such as Provisia® and Roxy-RPS® rice are needed to create a diverse weedy rice management ensemble available for rice production and move towards sustainable rice farming.
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Affiliation(s)
- Rasim Unan
- Department of Plant Science, University of California, Davis, 95616, CA, USA
| | - Ozgur Azapoglu
- Black Sea Agricultural Research Institute, Samsun, Türkiye
| | - İlyas Deligoz
- Black Sea Agricultural Research Institute, Samsun, Türkiye
| | - Husrev Mennan
- Plant Protection Department, Ondokuzmayis University, Samsun, Türkiye
| | - Kassim Al-Khatib
- Department of Plant Science, University of California, Davis, 95616, CA, USA.
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Manicardi A, Scarabel L, Llenes JM, Montull JM, Osuna MD, Torra Farré J, Milani A. Genetic basis and origin of resistance to acetolactate synthase inhibitors in Amaranthus palmeri from Spain and Italy. PEST MANAGEMENT SCIENCE 2023; 79:4886-4896. [PMID: 37515753 DOI: 10.1002/ps.7690] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/19/2023] [Accepted: 07/29/2023] [Indexed: 07/31/2023]
Abstract
BACKGROUND Amaranthus palmeri is an aggressive annual weed native to the United States, which has become invasive in some European countries. Populations resistant to acetolactate synthase (ALS) inhibitors have been recorded in Spain and Italy, but the evolutionary origin of the resistance traits remains unknown. Bioassays were conducted to identify cross-resistance to ALS inhibitors and a haplotype-based genetic approach was used to elucidate the origin and distribution of resistance in both countries. RESULTS Amaranthus palmeri populations were resistant to thifensulfuron-methyl and imazamox, and the 574-Leu mutant ALS allele was found to be the main cause of resistance among them. In two Spanish populations, 376-Glu and 197-Thr mutant ALS alleles were also found. The haplotype analyses revealed the presence of two and four distinct 574-Leu mutant haplotypes in the Italian and Spanish populations, respectively. None was common to both countries, but some mutant haplotypes were shared between geographically close populations or between populations more than 100 km apart. Wide genetic diversity was found in two very close Spanish populations. CONCLUSION ALS-resistant A. palmeri populations were introduced to Italy and Spain from outside Europe. Populations from both countries have different evolutionary histories and originate from independent introduction events. ALS resistance then spread over short and long distances by seed dispersal. The higher number and genetic diversity among mutant haplotypes from the Spanish populations indicated recurrent invasions. The implementation of control tactics to limit seed dispersal and the establishment of A. palmeri is recommended in both countries. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Alfredo Manicardi
- Department of Forestry and Agricultural Science and Engineering, University of Lleida, Lleida, Spain
| | - Laura Scarabel
- Institute for Sustainable Plant Protection (IPSP), CNR, Legnaro, Italy
| | - Josep María Llenes
- Weed Science Unit of the Plant Protection Service, DARP, Generalitat de Catalunya, Lleida, Spain
| | - José María Montull
- Department of Forestry and Agricultural Science and Engineering, University of Lleida, Lleida, Spain
| | - María Dolores Osuna
- Plant Protection Department, Extremadura Scientific and Technological Research Center (CICYTEX), Badajoz, Spain
| | - Joel Torra Farré
- Department of Forestry and Agricultural Science and Engineering, University of Lleida, Lleida, Spain
| | - Andrea Milani
- Institute for Sustainable Plant Protection (IPSP), CNR, Legnaro, Italy
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Cao Y, Lan Y, Huang H, Wei S, Li X, Sun Y, Wang R, Huang Z. Molecular Characterization of Resistance to Nicosulfuron in Setaria viridis. Int J Mol Sci 2023; 24:ijms24087105. [PMID: 37108267 PMCID: PMC10138712 DOI: 10.3390/ijms24087105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/04/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
The green foxtail, Setaria viridis (L.) P. Beauv. (Poales: Poaceae), is a troublesome and widespread grass weed in China. The acetolactate synthase (ALS)-inhibiting herbicide nicosulfuron has been intensively used to manage S. viridis, and this has substantially increased the selection pressure. Here we confirmed a 35.8-fold resistance to nicosulfuron in an S. viridis population (R376 population) from China and characterized the resistance mechanism. Molecular analyses revealed an Asp-376-Glu mutation of the ALS gene in the R376 population. The participation of metabolic resistance in the R376 population was proved by cytochrome P450 monooxygenases (P450) inhibitor pre-treatment and metabolism experiments. To further elucidate the mechanism of metabolic resistance, eighteen genes that could be related to the metabolism of nicosulfuron were obtained bythe RNA sequencing. The results of quantitative real-time PCR validation indicated that three ATP-binding cassette (ABC) transporters (ABE2, ABC15, and ABC15-2), four P450 (C76C2, CYOS, C78A5, and C81Q32), and two UDP-glucosyltransferase (UGT) (UGT13248 and UGT73C3), and one glutathione S-transferases (GST) (GST3) were the major candidates that contributed to metabolic nicosulfuron resistance in S. viridis. However, the specific role of these ten genes in metabolic resistance requires more research. Collectively, ALS gene mutations and enhanced metabolism may be responsible for the resistance of R376 to nicosulfuron.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - 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
| | - 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
| | - 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
| | - Ruolin Wang
- 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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Du Y, Wang M, Chen Y, Deng Y, Zhang L, Bai T, Ji M. Occurrence and mechanism of target-site resistance to bensulfuron-methyl in Monochoria korsakowii from China. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 191:105379. [PMID: 36963949 DOI: 10.1016/j.pestbp.2023.105379] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/18/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
Monochoria korsakowii is an increasingly significant threat to rice production across China, particularly in Liaoning province. Few studies have reported herbicide resistance in M. korsakowii, and resistance status and mechanisms are poorly understood. Here, thirty field populations of M. korsakowii were collected from 11 rice-growing regions of Liaoning, and 97% of populations had evolved resistance to bensulfuron-methyl (BM), with majority (24 of 28) showing high resistance levels (RI > 10). The first in-depth analysis of molecular features of AHAS1 and AHAS2 in BM-resistant populations showed that four Pro197 mutations (Pro197 to His, Ala, Leu or Ser) in AHAS1 and one mutation (Pro197Ser) in AHAS2 were identified. Notably, novel double Pro197Ser mutations co-occurred in both AHAS1 and AHAS2 in the most resistant line LN-20. Furthermore, resistant mutants were used to investigate the effect of Pro197 mutations on AHAS functionality, binding modes, gene expression and cross-resistance in M. korsakowii. All the detected Pro197 mutations considerably reduced in vitro AHAS sensitivity to BM by weakening hydrogen bonds and hydrophobic interactions in the predicted BM-AHAS complexes, especially the double Pro197Ser mutations. This novel resistance mutation combination slightly impacted the extractable AHAS activity, and increased the affinity and catalytic rate of pyruvate. Also, the AHAS expression level was significantly up-regulated. Moreover, all mutations provided resistance only to other sulfonylureas herbicides but not triazolopyrimidine or pyrimidinyl-benzoates herbicides. In conclusion, bensulfuron-methyl resistance in M. korsakowii was grim in Liaoning, China, and amino acid mutations on AHAS isozymes were the primary resistance mechanism. Double Pro197Ser mutations in both AHAS1 and AHAS2 confer higher herbicide resistance than single mutations in AHAS1. Thus, this work deepens our understanding of resistance status and mechanisms of M. korsakowii.
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Affiliation(s)
- Ying Du
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Minlong Wang
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Yan Chen
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Yunyan Deng
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Lulu Zhang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Tianlang Bai
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Mingshan Ji
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China.
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A LuALS Mutation with High Sulfonylurea Herbicide Resistance in Linum usitatissimum L. Int J Mol Sci 2023; 24:ijms24032820. [PMID: 36769141 PMCID: PMC9917167 DOI: 10.3390/ijms24032820] [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: 12/23/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
The cultivation of herbicide-resistant crops is an effective tool for weed management in agriculture. Weed control in flax (Linum usitatissimum L.) remains challenging due to the lack of available herbicide-resistant cultivars. In this study, a mutant resistant to acetolactate synthase (ALS)-inhibiting herbicides was obtained by ethyl methanesulphonate (EMS) mutagenesis using an elite cultivar, Longya10. Whole-plant dose-response assays revealed that, compared to Longya10, the mutant was 11.57-fold more resistant to tribenuron-methyl (TBM) and slightly resistant to imazethapyr (resistance index (mutant/Longya10) < 3). In vitro acetolactate synthase assays showed that the relative resistance of the mutant was 12.63 times more than that of Longya10. A biochemical analysis indicated that there was a Pro197Ser (relative to the Arabidopsis thaliana ALS sequence) substitution within the LuALS1, conferring high resistance to sulfonylurea herbicides in the mutant. Additionally, two cleaved amplified polymorphic sequence (CAPS) markers, BsaI-LuALS1 and EcoO109I-LuALS1, were developed based on the mutation site for marker assistant selection in breeding. Moreover, the mutant did not cause losses in natural field conditions. We find a mutant with ALS-inhibiting herbicide resistance chemically induced by EMS mutagenesis, providing a valuable germplasm for breeding herbicide-resistant flax varieties.
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Applications and Prospects of CRISPR/Cas9-Mediated Base Editing in Plant Breeding. Curr Issues Mol Biol 2023; 45:918-935. [PMID: 36826004 PMCID: PMC9955079 DOI: 10.3390/cimb45020059] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 system (Cas9) has been used at length to optimize multiple aspects of germplasm resources. However, large-scale genomic research has indicated that novel variations in crop plants are attributed to single-nucleotide polymorphisms (SNPs). Therefore, substituting single bases into a plant genome may produce desirable traits. Gene editing by CRISPR/Cas9 techniques frequently results in insertions-deletions (indels). Base editing allows precise single-nucleotide changes in the genome in the absence of double-strand breaks (DSBs) and donor repair templates (DRTs). Therefore, BEs have provided a new way of thinking about genome editing, and base editing techniques are currently being utilized to edit the genomes of many different organisms. As traditional breeding techniques and modern molecular breeding technologies complement each other, various genome editing technologies have emerged. How to realize the greater potential of BE applications is the question we need to consider. Here, we explain various base editings such as CBEs, ABEs, and CGBEs. In addition, the latest applications of base editing technologies in agriculture are summarized, including crop yield, quality, disease, and herbicide resistance. Finally, the challenges and future prospects of base editing technologies are presented. The aim is to provide a comprehensive overview of the application of BE in crop breeding to further improve BE and make the most of its value.
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