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Target-site mechanism confers resistance pattern of ACCase inhibitors in bearded sprangletop (Leptochloa fusca ssp. fascicularis) from California

Published online by Cambridge University Press:  31 May 2024

Rasim Unan
Affiliation:
Postdoctoral Researcher, Department of Plant Science, University of California, Davis, CA, USA
Aaron Becerra-Alvarez
Affiliation:
Graduate Student Researcher, Department of Plant Sciences, University of California, Davis, CA, USA
Kassim Al-Khatib*
Affiliation:
Professor, Department of Plant Sciences, University of California, Davis, CA, USA
*
Corresponding author: Kassim Al-Khatib; Email: kalkhatib@ucdavis.edu
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Abstract

Bearded sprangletop is a problematic native grass weed in California’s rice fields. The widespread and extensive use of acetyl-CoA carboxylase (ACCase)–inhibiting herbicides, such as cyhalofop-p-butyl (cyhalofop), has led to speculation that biotypes of bearded sprangletop have developed herbicide resistance to ACCase. The aim of this study was to evaluate suspected resistant bearded sprangletop biotypes, R1, R2, R3, and the susceptible biotype, S1, in terms of their levels of resistance to three ACCase-inhibiting herbicides and to characterize the molecular mechanisms of resistance. Dose–response experiments suggested that the biotype R1, R2, and R3 had high-level resistance to cyhalofop and to quizalofop-p-ethyl (quizalofop), but not clethodim. The study determined that the resistance to ACCase inhibitors was a target-site mechanism resulting from nucleotide substitution. The carboxyl transferase (CT) domain of the ACCase gene’s sequence analysis revealed the substitutions Trp-2027-Cys for R1 and R2 biotypes and Ile-2041-Asn for the R3 biotype. This study revealed the presence of target-site resistance to cyhalofop and quizalofop in at least two mutation points in representative biotypes of bearded sprangletop in California. This research highlights the significance of careful herbicide selection due to weed species responding quite rapidly to selection pressure, so as to aid in managing bearded sprangletop in rice fields.

Type
Research Article
Creative Commons
Creative Common License - CCCreative Common License - BY
This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited.
Copyright
© The Author(s), 2024. Published by Cambridge University Press on behalf of Weed Science Society of America

Introduction

Bearded sprangletop is one of the most common and competitive annual semiaquatic grasses, and it is widespread in California rice fields (Brim-DeForest et al. Reference Brim-DeForest, Al-Khatib and Fischer2017; Driver et al. Reference Driver, Al-Khatib and Godar2020a). Bearded sprangletop, an annual grass native to North America (Bryson and DeFelice Reference Bryson and DeFelice2009), relies on seed production to complete its life cycle. Bearded sprangletop produces many seeds, and seedlings generally emerge later than other weedy grasses (Driver et al. Reference Driver, Al-Khatib and Godar2020a; McCarty et al. Reference McCarty, Porter, Colvin, Shilling and Hall1995). Bearded sprangletop can reduce rice grain yield by up to 36% if not controlled (Smith Reference Smith1983). As a result of its prolificity and competitiveness, growers must manage this weed using cultural and chemical tools.

Although flooding rice fields with deep water is a common practice to suppress bearded sprangletop (Driver et al. Reference Driver, Al-Khatib and Godar2020a), herbicides are a major component of California’s weed control strategy to achieve adequate bearded sprangletop control and high rice yields (Yasuor et al. Reference Yasuor, TenBrook, Tjeerdema and Fischer2008). Despite the use of integrated weed management methods, bearded sprangletop biotypes in California have been suspected to be resistant to herbicides such as cyhalofop (Group 1, an ACCase inhibitor), thiobencarb [Group 15, an inhibitor of very-long-chain fatty acids (VLCFA) synthesis], clomazone (Group 13, an inhibitor of 1-deoxy-D-xyulose 5-phosphate (DXP) synthase], benzobicyclon + halosulfuron-methyl [Group 27, 7, 4-hydroxyphenylpyruvate dioxygenase (HPPD) + Group 2, acetolactate synthase (ALS) inhibitor] (Becerra-Alvarez et al. Reference Becerra-Alvarez, Godar, Ceseski and Al-Khatib2023; Brim-DeForest et al. Reference Brim-DeForest, Alarcon-Reverte and Fischer2015; Driver et al., Reference Driver, Al-Khatib and Godar2020b). Only clomazone resistance has been confirmed in bearded sprangletop biotypes (Driver et al. Reference Driver, Al-Khatib and Godar2020b). Preliminary studies by Brim-DeForest et al. (Reference Brim-DeForest, Alarcon-Reverte and Fischer2015) suggested target-site resistance to cyhalofop in bearded sprangletop. Therefore, identification of the resistance mechanisms might be useful in developing quick molecular diagnostic tests that advisors can use to confirm resistance development in bearded sprangletop.

ACCase inhibitors prevent plants from synthesizing fatty acids (Devine Reference Devine1997). Fatty acid synthesis inhibition likely prevents the creation of phospholipids needed to construct new membranes for cell development (Gronwald Reference Gronwald1991). Three catalytic domains make up ACCase: biotin carboxyl transferase (CT), biotin carboxylase (BC), and biotin carboxyl carrier (BCC) (Nikolskaya et al. Reference Nikolskaya, Zagnitko, Tevzadze, Haselkorn and Gornicki1999). These domains are all involved in the two reversible processes of carboxylation of acetyl-CoA. Initially, a biotin group covalently linked to the BCC domain is carboxylated in an ATP-dependent manner by the BC domain. Subsequently, the carboxyl group is transferred from biotin to acetyl-CoA by the CT domain. The biosynthesis of secondary metabolites and fatty acids depends on the produced malonyl-CoA (Harwood Reference Harwood1988). There are two distinct ACCase isoforms found in the plants. The homomeric enzyme cytosolic ACCase, present in all eukaryotes, combines the three domains into a single polypeptide. Most plants contain chloroplastic (plastidic) ACCase, a heterodimeric enzyme with three domains distributed among four subunits. Because their ACCase plastidic isoform is homomeric, plants belonging to the Poaceae family are unique (Konishi et al. Reference Konishi, Shinohara, Yamada and Sasaki1996). The selective binding of the CT domain of grasses’ plastidic isoform by aryloxyphenoxypropionates (FOPs), the cyclohexanediones (DIMs), and the phenylpyrazolin herbicides confers herbicidal effects; other isoforms remain unaffected and insensitive (Kaundun et al. Reference Kaundun, Hutchings, Dale and McIndoe2013; Nikolskaya et al. Reference Nikolskaya, Zagnitko, Tevzadze, Haselkorn and Gornicki1999; Zhang et al. Reference Zhang, Tweel and Tong2004). Long-term usage of FOPs herbicides, particularly in rice production, has exerted selection pressure on weeds and led to resistant bearded sprangletop biotypes (Phongphitak et al. Reference Phongphitak, Maneechote, Rerkasem and Jamjod2014; Rahman et al. Reference Rahman, Ismail and Sofian-Azirun2011). Cyhalofop, quizalofop, and clethodim are typically used to control grass as a FOPs and DIMs herbicides. Cyhalofop is widely used in conventional rice farming systems, and quizalofop is utilized in Provisia® rice farming system to control bearded sprangletop, other weed grasses, and weedy rice (Lancaster et al. Reference Lancaster, Norsworthy and Scott2018).

The fundamental source of the weeds’ resistance is attributed to the development of target- and/or non–target-site resistance mechanisms to herbicides (Délye et al. Reference Délye, Jasieniuk and LeCorre2013). Target-site resistance and non–target-site resistance mechanisms can contribute to weed survival, depending on the selections made to its genetic changes (Délye et al. Reference Délye, Jasieniuk and LeCorre2013). Target-site and non–target-site resistance mechanisms can also coexist in a single individual or population, raising their resistance to one herbicide or giving them multiple resistance to various herbicides (Garcia et al. Reference Garcia, Palma-Bautista, Rojano-Delgado, Bracamonte, Portugal, Alcantara-de la Cruz and De Prado2019). Target-site resistance constitutes the most common resistance mechanism to ACCase (Powles and Yu Reference Powles and Yu2010). Herbicide target-site amino acid substitution in the CT domain of ACCase has caused herbicide resistance in various weed species (Laforest et al. Reference Laforest, Soufiane, Simard, Obeid, Page and Nurse2017). Several amino acid substitutions have been reported in the ACCase gene region in resistant Leptochloa spp. such as Ile-1781-Leu, Ile-1781-Trp, Trp-1999-Cys, Trp-2027-Ser, Trp-2027-Leu, Trp-2027-Cys, Ile-2041-Asn, Asp-2078-Gly, Cys-2088-Arg, Gly-2096-Ala (Deng et al. Reference Deng, Cai, Zhang, Chen, Chen, Di and Yuan2019; Peng et al. Reference Peng, Pan, Liu, Cheng, Ma, Li, Liu, Wang and Bai2020; Yu et al. Reference Yu, Collavo, Zheng, Owen, Sattin and Powles2007, Reference Yu, Gao, Pan, Yao and Dong2017; Yuan et al. Reference Yuan, Di, Chen, Chen, Cai and Deng2019; Zhang et al. Reference Zhang, Chen, Xu, Song, Yao, Gao and Wu2020; Zhao et al. Reference Zhao, Jiang, Li, Gao, Zhang, Liao and Cao2022).

Recently, suspected herbicide-resistant bearded sprangletop biotypes have become a common problem in California rice fields. In annual survey studies conducted in California, Becerra-Alvarez et al. (Reference Becerra-Alvarez, Godar, Ceseski and Al-Khatib2023) observed an increase in suspected cyhalofop-resistant bearded sprangletop biotypes. This research examines the resistance of three bearded sprangletop biotypes to ACCase-inhibiting herbicides. Specifically, this study aimed to confirm resistance and determine the resistance level of the three suspected bearded sprangletop biotypes through the development of dose–response curves to cyhalofop, quizalofop, and clethodim. The second objective was to establish whether a mutation in the target-site gene was responsible for resistance.

Materials and Methods

Plant Material

A total of four bearded sprangletop biotypes, one known susceptible (S1) and three suspected resistant (R1, R2, and R3) to cyhalofop, were studied. Bearded sprangletop biotype S1 (ST-HR-2015) was collected from California Rice Experiment Station in Biggs, CA (39.451999°N; 121.72417°W) in 2015, and its new generation was produced in the greenhouse in 2019. Suspected resistant bearded sprangletop biotypes were collected from rice fields with a history of cyhalofop use and where bearded sprangletop survived the herbicide treatment. R1 (ST-19-10) was collected from Butte County, CA (39.379639°N; 121.744028°W) in 2019; R2 (ST-20-02) was collected from Glenn County, CA (39.626306°N; 122.03722°W) in 2020; and R3 (ST-21.07) was collected from Colusa County, CA (39.318667°N; 122.121722°W) in 2021. The seeds were stored at 4 C until utilized in the experiments. To break bearded sprangletop seed dormancy, seeds were placed in a freezer at –20 C for 3 mo before being placed in a refrigerated test tube at 4 C and soaked in deionized water. The water in the tubes was changed daily for 2 wk (Driver et al. Reference Driver, Al-Khatib and Godar2020b). The seeds were then placed on wet filter paper and incubated for 16 h at 40 C. Germinated seeds were transplanted in 8-cm by 8-cm by 6-cm pots in the greenhouse on Orchard Park Drive at UC Davis. Three seedlings were placed in each pot. Greenhouse temperature was 23 to 34 C, relative humidity was 65% to 70%, and 14-h/10-h day/night photoperiod. The supplemental light was 400 µmol m–2 s–1. Sterilized media soil was used, composed of one part compost (redwood shavings and turkey manure), one part coarse sand, one part peat moss, and 1.23 kg m–3 dolomite. The soil pH was 6.6, and the soil nutrient was 125 mg kg–1 available N, P2O5 46 mg kg–1 Olsen P, 759 mg kg–1 extractable K, 1,041 mg kg–1 calcium, 578 mg kg–1 magnesium, 7.6 mg kg–1 copper, 13 mg kg–1 zinc, 58 mg kg–1 manganese, 57 mg kg–1 iron, and 0.51 mg kg–1 boron. Plants were irrigated as needed.

Dose-Response Experiment

Herbicides were applied at three- to four-leaf stage. Cyhalofop, quizalofop, and clethodim doses were selected 16-fold below and above the label dose of herbicide with the control application, thus, 0×, 1/16×, 1/8×, 1/4×, 1/2×, 1×, 2×, 4×, 8×, and 16× (Table 1). Cyhalofop-p-butyl ((2R)-2-[4-(4-cyano-2-fluorophenoxy) phenoxy] propanoate) formulation was Clincher CA (Corteva Agriscience, Indianapolis, IN), which contained 29.6% of active ingredient. Cyhalofop was applied with 2.5% crop oil concentrate (COC). Quizalofop-p-ethyl (2-[4-(6-chloroquinoxalin-2-yl) oxyphenoxy] propanoate) formulation was Targa (Nissan Chemical Corporation, Japan), which contained 10.3% active ingredient. Quizalofop was applied with 1% COC. Clethodim (2-[(E)-N-[(E)-3-chloroprop-2-enoxy]-C-ethylcarbonimidoyl]-5-(2-ethylsulfanylpropyl)-3-hydroxycyclohex-2-en-1-one) herbicide formulation was Select Max (Valent U.S.A. LLC, San Ramon, CA), which contained 12.6% of the active ingredient. Clethodim was applied with 0.25% nonionic surfactant. Adjuvants were selected according to product labels, and their application was based on percent volume per volume (%v/v) concentration. Herbicides were applied in a spray chamber (Technical Machinery Inc., Berkeley, CA) with one Teejet XR8002VS flat-fan nozzle (TeeJet Tech., Springfield, IL) calibrated to deliver 187 L ha–1 at 275 kPa pressure; application height of the nozzle was 72 cm, and speed was 1.34 m s–1. After herbicide application, pots were placed back inside the greenhouse and irrigated 48 h later. Pots were maintained until harvest, and the aboveground plants were harvested 28 d after treatment. Plants were dried at 70 C for 3 d. The herbicide dose required to control 50% of the test biotypes (ED50) was calculated from dry-plant weight and converted to dry-biomass percentage compared to the nontreated control for presentation (Seefeldt et al. Reference Seefeldt, Jensen and Fuerst1995). The experiment was conducted twice as a randomized block design with three replications.

Table 1. Clethodim, cyhalofop-p-butyl and quizalofop-p-ethyl application doses used in this study on the suspected herbicide-resistant bearded sprangletop biotypes.

Nucleotide Substitution Experiment

Fresh leaf tissue from five plants of each bearded sprangletop biotype were collected at 28 d after treatment. Cetyltrimethylammonium bromide DNA extraction method was used (Doyle and Doyle Reference Doyle and Doyle1987). Two primer pairs were designed based on sequences of Leptochloa chinensis (L.) Nees (GenBank: QWJ75145.1) from the National Center for Biotechnology Information (Table 2). The expected coverage of the two pairs was 98.9% and the 643 number of nucleotides they overlap. Polymerase chain reaction (PCR) amplification was performed using the Qiagen Taq PCR master mix (Qiagen, N.V., Netherlands), which contained 25 μL TAq Master mix, 1 μL of each primer (10 μM), 1 μL genomic DNA mixed in ddH2O in 50 μL. Thermal was included initially as denaturing step at 95 C for 5 min, followed by 35 cycles of 45 s denaturation at 95 C, 45 s annealing at 60 C, 60 s elongation at 72 C, and a final extension of 5 min at 72 C. Electrophoresis was performed at 120 V for 1 h. Plant DNA was purified by QIAquick PCR Purification Kit (Qiagen, N.V., Nederlands). Sequencing was performed at UC Davis Genomic Center. The sequencing data were analyzed by using MEGA 11: Molecular Evolutionary Genetics Analysis version 11 (Tamura et al. Reference Tamura, Stecher and Kumar2021).

Table 2. Primers of the ACCase gene fragment of bearded sprangletop.

Statistical Analyses

A four-parameter log-logistic model (Eq. 1) was used to establish the dose of each herbicide that result in 50% dry-weight reduction (ED50) (Seefeldt et al. Reference Seefeldt, Jensen and Fuerst1995). The ED50 estimations were computed using the R DRC package (v4.3-1; Ritz et al. Reference Ritz, Baty, Streibig and Gerhard2015) for statistical analysis.

(1) $$Y = C + {{D - C} \over {1 + exp(b({\rm{log}}(x) - {\rm{log}}(E{D_{50}})))}}$$

where Y is biomass, b is the slope at the inflexion point (ED50), C and D are the lower and higher boundaries of the asymptote, respectively, and x is the herbicide dose. ANOVA was used to examine the P value that indicated a significant difference between the S and R biotypes. The resistance index (RI) was computed by dividing the ED50 of the resistant biotype by that of the susceptible biotype (Guo et al. Reference Guo, Lv, Zhang, Li, Wu, Lu, Liu and Wang2016).

Results and Discussion

Dose–Response Study

All three bearded sprangletop biotypes were found to exhibit high-level resistance to cyhalofop. The ED50 value for susceptible bearded sprangletop (S1) treated with cyhalofop was 27.4 g ai ha–1; however, the R1, R2, and R3 resistant biotypes had ED50 values higher than 4,480 g ai ha–1 cyhalofop (16×), resulting in RI values more than 164-fold (Table 3). The exact ED50 values could not be calculated for R1, R2, and R3, resistant to cyhalofop (Table 3, Figure 1), as bearded sprangletop survived at all cyhalofop doses applied with no 50% reduction in dry weight.

Table 3. Average cyhalofop, quizalofop, and clethodim dose that cause 50% dry-weight reduction (ED50) and resistance index (RI) of bearded sprangletop biotypes.

a SE, standard error, which is an average of two runs. >4,480 and >1,792, the data did not allow for the estimation of ED50 values, as all doses of cyhalofop and quizalofop were not sufficient to cause a 50% reduction in dry weight.

b RI, resistance index ED50 value of resistant bearded sprangletop biotype divided by that of susceptible biotype.

Figure 1. Effect of cyhalofop on the growth biomass of R1 (Δ), R2 (+), R3 (×), and S (o) biotypes of bearded sprangletop. S was the susceptible biotype; R1, R2, and R3 were resistant biotypes. Each point represents the average of six measurements (two runs and three replications) with standard error of the mean. Dose–response curves were generated by nonlinear regression using a log-logistic model. Vertical error bars represent the 95% confidence intervals at ED50.

It was determined that all three bearded sprangletop biotypes showed high levels of resistance to quizalofop. Whereas all resistant biotypes showed dry-weight reduction between 30% and 70% even at the highest dose of 1,792 g ai ha–1 (16×) quizalofop, no S1 plants could not maintain their dry weight at 112 g ai ha–1 (1×) quizalofop (Table 3, Figure 2). The S1 biotypes had ED50 of 12.0 g ai ha–1 quizalofop, but the R2 resistant biotype had ED50 values higher than 1,792 g ai ha–1 (16×), resulting in RI values more than 150-fold (Table 3). The exact ED50 values could not calculated for resistant R2 biotype as a result of high resistance to quizalofop and no 50% reduction in dry weight (Figure 2). Bearded sprangletop biotypes R1 and R3 exhibited ED50 values of 1,107.8 and 602.1 g ai ha–1 to quizalofop, respectively.

Figure 2. Effect of quizalofop on the growth biomass of R1 (Δ), R2 (+), R3 (×), and S (o) biotypes of bearded sprangletop. S was the susceptible biotype; R1, R2, and R3 were resistant biotypes. Each point represents the average of six measurements (two runs and three replications) with standard error of the mean. Dose–response curves were generated by nonlinear regression using a log-logistic model. Vertical error bars represent the 95% confidence intervals at ED50.

It is evident that the cyhalofop and quizalofop doses used in this study were not high enough to significantly reduce the dry weight of the resistant biotypes. However, the doses used in this study were similar to those used in previous research that examined herbicide resistance in Leptochloa spp. (Brim-Deforest et al. Reference Brim-DeForest, Alarcon-Reverte and Fischer2015; Deng et al. Reference Deng, Cai, Zhang, Chen, Chen, Di and Yuan2019; Peng et al. Reference Peng, Pan, Liu, Cheng, Ma, Li, Liu, Wang and Bai2020; Tehranchian et al. Reference Tehranchian, Norsworthy, Korres, McElroy, Chen and Scott2016; Yuan et al. Reference Yuan, Tian, Li, Qian, Guo and Shen2021; Zhang et al. Reference Zhang, Chen, Song, Zhang, Xu and Wu2022).

For clethodim, all bearded sprangletop biotypes were killed at 1× dose. S1, R1, R2, and R3 biotypes had ED50 values of 20.9, 24.3, 23.6, and 20.7 g ai ha–1 clethodim, respectively (Figure 3). Therefore, the R biotypes were susceptible to clethodim despite being resistant to the two APP (FOP) herbicides.

Figure 3. Effect of clethodim on the growth biomass of R1 (Δ), R2 (+), R3 (×), and S (o) biotypes of bearded sprangletop. S1, R1, R2, and R3 were all susceptible to clethodim. Each point represents the average of six measurements (two runs and three replications) with standard error of the mean. Dose–response curves were generated by nonlinear regression using a log-logistic model. Vertical error bars represent the 95% confidence intervals at ED50.

One of the main herbicides used since 2003 in California rice fields to control bearded sprangletop has been cyhalofop. ACCase inhibitor–resistant biotypes may emerge after 6 to 10 yr of selection pressure, especially in cropping systems where the ongoing use of these herbicides is the sole method of controlling grass weeds (Devine Reference Devine1997). With the frequent and intense use of cyhalofop in California rice fields, the continuous rice cultivation year after year, and a limited number of available herbicides, it is not surprising that bearded sprangletop has developed resistance to cyhalofop (Becerra-Alvarez et al. Reference Becerra-Alvarez, Godar, Ceseski and Al-Khatib2023; Brim-DeForest et al. Reference Brim-DeForest, Alarcon-Reverte and Fischer2015). This study revealed that suspected resistant bearded sprangletop biotypes, R1, R2, and R3, had a high level of resistance to cyhalofop and quizalofop but not to clethodim in California rice fields. This study also suggested that quizalofop, used in the newly developed Provisia rice technology, will have problems combating resistant bearded sprangletop in California. The Provisia system features a non-GMO herbicide-tolerant rice, allowing growers to safely apply quizalofop (Mankin et al. Reference Mankin, Neuteboom, Whitt, Schoefl, Hong, Wenck, Carlson, McElver and Stevenson–Paulik2021). Although clethodim is not registered in rice, it is understood to be used successfully to control bearded sprangletop and other economically important weeds with spot spray applications (Unan et al. Reference Unan, Galvin, Becerra-Alvarez and Al-Khatib2024). In addition, this study may indicate that clethodim could be a useful tool to control bearded sprangletop if clethodim-resistant rice is developed. However, one must consider the possibility that other biotypes might have resistance to clethodim after selection with cyhalofop and that clethodim, if used the same way, could exert a strong selection pressure.

Target-Site Resistance: ACCase Mutation Detection

Each biotype of bearded sprangletop provided partial ACCase gene sequences. The results of a sequence alignment revealed a 98.8% similarity between the ACCase gene sequences from bearded sprangletop and Leptochloa chinensis (L.) Nees (GenBank:QWJ75145.1). All tested plants of the R1 and R2 biotypes displayed a substitution of Ile (ATT) to Asn (AAT) at position Ile-2041-Asn, whereas R3 biotype displayed a substitution of Trp (TGG) to Cys (TGC) at position Trp-2027-Cys compared with the S1 biotype and Leptochloa chinensis (L.) Nees. The plants from the S1 biotype, meanwhile, showed no signs of any known mutation.

Target-site–based resistance mechanisms frequently make for cross-resistance to herbicides that have the same mode of action (Beckie and Tardif Reference Beckie and Tardif2012). Several ACCase mutation points in bearded sprangletop have been reported so far. The present study identified two distinct ACCase mutations, Trp-2027-Cys and Ile-2041-Asn, for bearded sprangletop (Figure 4). The Ile-2041-Asn substitution was found in R1 and R2, whereas the Trp-2027-Cys substitution was found in R3, but these substitutions have been reported before as conferring plants with resistance to FOPs and susceptibility to clethodim (Yu et al. Reference Yu, Collavo, Zheng, Owen, Sattin and Powles2007). Though the Trp-2027-Cys substitution has been documented before in bearded sprangletop from California (Brim-DeForest et al. Reference Brim-DeForest, Alarcon-Reverte and Fischer2015), this is the first occurrence of the Ile-2041-Asn substitution. Tehranchian et al. (Reference Tehranchian, Norsworthy, Korres, McElroy, Chen and Scott2016) previously identified mutations in the Amazon sprangletop in Trp-2027-Cys in Arkansas. Zhao et al. (Reference Zhao, Jiang, Li, Gao, Zhang, Liao and Cao2022) identified Trp-2027-Cys substitution in Leptochloa chinensis sprangletop and noted that it was resistant to cyhalofop. In addition, Peng et al. (Reference Peng, Pan, Liu, Cheng, Ma, Li, Liu, Wang and Bai2020) reported Trp-2027-Ser and Ile-2041-Asn mutations in which it was resistant to cyhalofop in Leptochloa chinensis. Moreover, Yuan et al. (Reference Yuan, Di, Chen, Chen, Cai and Deng2019) detected Gly-2096-Ala substitution in Diplachne fusca, but this substitution was not detected in our study.

Figure 4. ACCase amino acid sequences of the amplified fragment of Leptochloa chinensis (L.) Nees, the susceptible (S1) and resistant (R1, R2, and R3) biotypes of bearded sprangletop. The black boxes illustrate the amino acid substitution from tryptophan (W) 2027 to cytosine (C) in R1 and R2, and from isoleucine (I) 2041 to leucine (N) in R3. The Leptochloa chinensis (L.) Nees (GenBank: QWJ75145.1) and susceptible bearded sprangletop (S1) ACCase sequence were used as references.

Cyhalofop is the only postemergence herbicide available in California to control bearded sprangletop; however, there are preemergence herbicides to control this weed, including clomazone, thiobencarb, and benzobicyclon (Becerra-Alvarez et al. Reference Becerra-Alvarez, Godar, Ceseski and Al-Khatib2023). If cyhalofop resistance is known in the field, then using preemergence herbicides becomes essential.

Practical Implications

In conclusion, bearded sprangletop resistance to selected ACCase inhibitors is present in California rice fields. The bearded sprangletop biotypes under study were resistant to cyhalofop and quizalofop, but not to clethodim. Target-site resistance was identified as the primary factor contributing to the resistance to cyhalofop and quizalofop for bearded sprangletop. The Trp-2027-Cys and Ile-2041-Asn target-site substitutions play a crucial role in the resistance to cyhalofop and quizalofop for bearded sprangletop in California. The results can aid in creating scientific approaches for the integrated management of resistant biotypes to ACCase inhibitors in bearded sprangletop. This study also revealed that all tested biotypes were susceptible to clethodim. The possibility of resistant bearded sprangletop genotypes becoming widespread in the coming years may cause greater problems. It might be suggested to rice farmers that integrated weed management such as crop rotation, certified clean seeds, deep flooding (Driver et al. Reference Driver, Al-Khatib and Godar2020a), tilling the soil no more than 20 cm deep, and spot spray application (Unan et al. Reference Unan, Galvin, Becerra-Alvarez and Al-Khatib2024) to control of resistant bearded sprangletop.

Acknowledgments

This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. [897192], (project HerbaRice). This paper was given in part during the “100th Anniversary Turkish Herbology Congress” in 2023.

The authors declare no conflicts of interest.

Footnotes

Associate Editor: R. Joseph Wuerffel, Syngenta

References

Becerra-Alvarez, A, Godar, AS, Ceseski, AR, Al-Khatib, K (2023) Herbicide resistance management in rice: annual field survey of California rice weeds helps establish a weed management decision framework. Outlook Pest Manag 34:5157 Google Scholar
Beckie, HJ, Tardif, FJ (2012) Herbicide cross resistance in weeds. Crop Prot 35:1528 Google Scholar
Brim-DeForest, W, Al-Khatib, K, Fischer, AJ (2017) Predicting yield losses in rice mixed-weed species infestations in California. Weed Sci 65:6172 Google Scholar
Brim-DeForest, W, Alarcon-Reverte, R, Fischer, AJ (2015) Resistance of Leptochloa fusca spp. fascicularis (bearded sprangletop) to ACCase inhibitors in California rice. Page 82 in Proceedings of the 67th California Weed Science Society. Santa Barbara, CA: California Weed Science SocietyGoogle Scholar
Bryson, CT, DeFelice, MS, eds. (2009) Weeds of the South. Athens, GA: University of Georgia Press.Google Scholar
Délye, C, Jasieniuk, M, LeCorre, V (2013) Deciphering the evolution of herbicide resistance in weeds. Trends Genet 29:649658 Google Scholar
Deng, W, Cai, JX, Zhang, JY, Chen, YY, Chen, YR, Di, YJ, Yuan, SZ (2019) Molecular basis of resistance to ACCase-inhibiting herbicide cyhalofop butyl in Chinese sprangletop (Leptochloa chinensis (L.) Nees) from China. Pestic Biochem Physiol 158:143148 Google Scholar
Devine, MD (1997) Mechanisms of resistance to acetyl-coenzyme A carboxylase inhibitors: a review. Pestic Sci 51:259264 Google Scholar
Doyle, JJ, Doyle, JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:1115 Google Scholar
Driver, K, Al-Khatib, K, Godar, A (2020a) Bearded sprangletop (Diplachne fusca ssp. fascicularis) flooding tolerance in California rice. Weed Technol 34:193196 Google Scholar
Driver, KE, Al-Khatib, K, Godar, A (2020b) Survey of bearded sprangletop (Leptochloa fusca spp. fasicularis) response to clomazone in California rice. Weed Technol 34:661665 Google Scholar
Garcia, MJ, Palma-Bautista, C, Rojano-Delgado, AM, Bracamonte, E, Portugal, J, Alcantara-de la Cruz, R, De Prado, R (2019) The triple amino acid substitution TAP-IVS in the EPSPS gene confers high glyphosate resistance to the superweed Amaranthus hybridus. Int J Mol Sci 20:2396 Google Scholar
Gronwald, JW (1991) Lipid biosynthesis inhibitors. Weed Sci 39:435449 Google Scholar
Guo, WL, Lv, LL, Zhang, LL, Li, Q, Wu, CX, Lu, XT, Liu, W, Wang, J (2016) Herbicides cross resistance of a multiple resistant shortawn foxtail (Alopecurus aequalis Sobol.) population in wheat field. Chil J Agric Res 76:163169 Google Scholar
Harwood, JL (1988) Fatty acid metabolism. Annu Rev Plant Physiol Plant Mol Biol 39:101138 Google Scholar
Kaundun, SS, Hutchings, SJ, Dale, RP, McIndoe, E (2013) Role of a novel I1781T mutation and other mechanisms in conferring resistance to acetyl-CoA carboxylase inhibiting herbicides in a black-grass population. PLoS One 8:e69568 Google Scholar
Konishi, T, Shinohara, K, Yamada, K, Sasaki, Y (1996) Acetyl-coA carboxylase in higher plants: most plants other than Gramineae have both the prokaryotic and the eukaryotic forms of this enzyme. Plant Cell Physiol 37:117122.Google Scholar
Laforest, M, Soufiane, B, Simard, MJ, Obeid, K, Page, E, Nurse, RE (2017) Acetyl-CoA carboxylase overexpression in herbicide-resistant large crabgrass (Digitaria sanguinalis). Pest Manag Sci 73:22272235 Google Scholar
Lancaster, ZD, Norsworthy, JK, Scott, RC (2018) Evaluation of quizalofop-resistant rice for Arkansas rice production systems. Int J Agron 6315865:8Google Scholar
Mankin, SL, Neuteboom, L, Whitt, SR, Schoefl, U, Hong, H, Wenck, A, Carlson, DR, McElver, JA, Stevenson–Paulik, JM, Inventor; BASF SE, assignee (2021) August 24. Method for treating post-emergent rice. US patent 11,096,345B2Google Scholar
McCarty, LB, Porter, DW, Colvin, DL, Shilling, DG, Hall, DW (1995) Controlling two sprangletop (Leptochloa spp.) species with preemergence herbicides. Weed Technol 9:2933 Google Scholar
Nikolskaya, T, Zagnitko, O, Tevzadze, G, Haselkorn, R, Gornicki, P (1999) Herbicide sensitivity determinant of wheat plastid acetyl-CoA carboxylase is located in a 400–amino acid fragment of the carboxyltransferase domain. PNAS USA 96:1464714651 Google Scholar
Peng, YJ, Pan, L, Liu, DC, Cheng, XM, Ma, GL, Li, SF, Liu, XY, Wang, LF, Bai, LY (2020) Confirmation and characterization of cyhalofop-butyl–resistant Chinese sprangletop (Leptochloa chinensis) populations from China. Weed Sci 68:253259 Google Scholar
Phongphitak, E, Maneechote, C, Rerkasem, B, Jamjod, S (2014) Inheritance of resistance to fenoxaprop-p-ethyl in sprangletop (Leptochloa chinensis L. Nees). Weed Biol Manag 14:159166 Google Scholar
Powles, SB, Yu, Q (2010) Evolution in action: plants resistant to herbicides. Annu Rev Plant Biol 61:317347 Google Scholar
Rahman, MM, Ismail, S, Sofian-Azirun, M (2011) Identification of resistant biotypes of Leptochloa chinensis in rice field and their control with herbicides. Afr J Biotechnol 10:29042914 Google Scholar
Ritz, C, Baty, F, Streibig, JC, Gerhard, D (2015) Dose–response analysis using R. PloS One 10:e0146021 Google Scholar
Seefeldt, SS, Jensen, JE, Fuerst, EP (1995) Log-logistic analysis of herbicide dose–response relationships. Weed Technol 9:218227 Google Scholar
Smith, RJ (1983) Competition of bearded sprangletop (Leptochloa fascicularis) with rice (Oryza sativa). Weed Sci 31:120123 Google Scholar
Tamura, K, Stecher, G, Kumar, S (2021) MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 38:30223027 Google Scholar
Tehranchian, P, Norsworthy, JK, Korres, NE, McElroy, S, Chen, S, Scott, RC (2016) Resistance to aryloxyphenoxypropionate herbicides in Amazon sprangletop: confirmation, control, and molecular basis of resistance. Pestic Biochem Phys 133:7984 Google Scholar
Unan, R, Galvin, L, Becerra-Alvarez, A, Al-Khatib, K (2024) Assessing clethodim spot spraying applications for control of problematic weedy rice and other grasses in California rice fields. Agron J 116:302312 Google Scholar
Yasuor, H, TenBrook, PL, Tjeerdema, RS, Fischer, AJ (2008) Responses to clomazone and 5-ketoclomazone by Echinochloa phyllopogon resistant to multiple herbicides in Californian rice fields. Pest Manag Sci 64:10311039 Google Scholar
Yu, JX, Gao, HT, Pan, L, Yao, ZW, Dong, LY (2017) Mechanism of resistance to cyhalofop-butyl in Chinese sprangletop (Leptochloa chinensis (L.) Nees). Pestic Biochem Physiol 143:306311 Google Scholar
Yu, Q, Collavo, A, Zheng, MQ, Owen, M, Sattin, M, Powles, SB (2007) Diversity of acetyl-coenzyme A carboxylase mutations in resistant Lolium populations: evaluation using clethodim. J Plant Physiol 145:547558 Google Scholar
Yuan, G, Tian, Z, Li, T, Qian, Z, Guo, W, Shen, G (2021) Cross-resistance pattern to ACCase-inhibiting herbicides in a rare Trp-2027-Ser mutation Chinese sprangletop (Leptochloa chinensis) population. Chil J Agric Res 81:6269 Google Scholar
Yuan, S, Di, Y, Chen, Y, Chen, Y, Cai, J, Deng, W (2019) Target-site resistance to cyhalofop-butyl in bearded sprangletop (Diplachne fusca) from China. Weed Sci 67:534538 Google Scholar
Zhang, H, Tweel, B, Tong, L (2004) Molecular basis for the inhibition of the carboxyltransferase domain of acetylcoenzyme-A carboxylase by haloxyfop and diclofop. PNAS USA 101:59105915.Google Scholar
Zhang, Y, Chen, LP, Xu, BQ, Song, W, Yao, XM, Gao, JL, Wu, CX (2020) Resistance of Leptochloa chinensis (L.) Nees to cyhalofop-butyl and metamifop in rice fields of Zhejiang Province and involved molecular mechanism. Chin J Pestic Sci 22:447453 Google Scholar
Zhang, Y, Chen, L, Song, W, Zhang, T, Xu, M, Wu, C (2022) Diverse mechanisms associated with cyhalofop-butyl resistance in Chinese sprangletop (Leptochloa chinensis (L.) Nees): characterization of target-site mutations and metabolic resistance-related genes in two resistant populations. Front Plant Sci 13:990085 Google Scholar
Zhao, N, Jiang, MH, Li, Q, Gao, Q, Zhang, JX, Liao, M, Cao, HQ (2022) Cyhalofop-butyl resistance conferred by a novel Trp-2027-Leu mutation of acetyl-CoA carboxylase and enhanced metabolism in Leptochloa chinensis . Pest Manag Sci 78:11761186 Google Scholar
Figure 0

Table 1. Clethodim, cyhalofop-p-butyl and quizalofop-p-ethyl application doses used in this study on the suspected herbicide-resistant bearded sprangletop biotypes.

Figure 1

Table 2. Primers of the ACCase gene fragment of bearded sprangletop.

Figure 2

Table 3. Average cyhalofop, quizalofop, and clethodim dose that cause 50% dry-weight reduction (ED50) and resistance index (RI) of bearded sprangletop biotypes.

Figure 3

Figure 1. Effect of cyhalofop on the growth biomass of R1 (Δ), R2 (+), R3 (×), and S (o) biotypes of bearded sprangletop. S was the susceptible biotype; R1, R2, and R3 were resistant biotypes. Each point represents the average of six measurements (two runs and three replications) with standard error of the mean. Dose–response curves were generated by nonlinear regression using a log-logistic model. Vertical error bars represent the 95% confidence intervals at ED50.

Figure 4

Figure 2. Effect of quizalofop on the growth biomass of R1 (Δ), R2 (+), R3 (×), and S (o) biotypes of bearded sprangletop. S was the susceptible biotype; R1, R2, and R3 were resistant biotypes. Each point represents the average of six measurements (two runs and three replications) with standard error of the mean. Dose–response curves were generated by nonlinear regression using a log-logistic model. Vertical error bars represent the 95% confidence intervals at ED50.

Figure 5

Figure 3. Effect of clethodim on the growth biomass of R1 (Δ), R2 (+), R3 (×), and S (o) biotypes of bearded sprangletop. S1, R1, R2, and R3 were all susceptible to clethodim. Each point represents the average of six measurements (two runs and three replications) with standard error of the mean. Dose–response curves were generated by nonlinear regression using a log-logistic model. Vertical error bars represent the 95% confidence intervals at ED50.

Figure 6

Figure 4. ACCase amino acid sequences of the amplified fragment of Leptochloa chinensis (L.) Nees, the susceptible (S1) and resistant (R1, R2, and R3) biotypes of bearded sprangletop. The black boxes illustrate the amino acid substitution from tryptophan (W) 2027 to cytosine (C) in R1 and R2, and from isoleucine (I) 2041 to leucine (N) in R3. The Leptochloa chinensis (L.) Nees (GenBank: QWJ75145.1) and susceptible bearded sprangletop (S1) ACCase sequence were used as references.