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. 2026 Jul 15;82(10):10185–10191. doi: 10.1002/ps.71056

Persistence of PPO mutations and dynamics of Amaranthus palmeri resistance to PPO‐inhibitor herbicides in a decade

Prakriti Dhaka 1,2,†, Gulab Rangani 1,†, Aimone Porri 3, Ingo Meiners 4, Robert C Scott 1, Nilda Roma‐Burgos 1,✉
PMCID: PMC13569166  PMID: 42458731

Abstract

BACKGROUND

Amaranthus is a highly troublesome weed genera globally. Most cotton, corn, and soybean fields in the US mid‐south have Amaranthus palmeri populations resistant to protoporphyrinogen oxidase (PPO)‐inhibiting herbicides. We evaluated the persistence of resistance to PPO‐inhibiting herbicides in A. palmeri populations from Greene (GRE‐A) and Crittenden (CRI‐D) counties, Arkansas, collected in 2015 and approximately 8 years later.

RESULTS

Fomesafen, the primary selector for resistance to PPO‐inhibiting herbicides, was the least effective herbicide in both post‐ and pre‐emergence tests. Soil‐applied sulfentrazone was more effective on GRE‐A than CRI‐D populations. Fomesafen was less effective on CRI‐D than GRE‐A populations. GRE‐A populations were more resistant to foliar‐applied PPO‐inhibiting herbicides (62–76% control) than CRI‐D populations. Resistance to fomesafen in CRI‐D increased significantly with time, declining from 91% control in 15‐CRI‐D to 48% in 22‐CRI‐D. GRE‐A populations harbored high frequencies of ΔG210 and A399 mutations. CRI‐D populations predominantly harbored ΔG210 and G128 mutations. Increased resistance to fomesafen was strongly linked to increased frequency of single mutations, primarily ΔG210. Resistance to foliar‐applied flumioxazin lacked a clear association with target‐site mutations, while resistance to saflufenacil was associated with enrichment of double mutations.

CONCLUSIONS

PPO2 mutations remained the primary factor conferring resistance to PPO‐inhibiting herbicides over 8 years, underscoring their evolutionary advantage in maintaining A. palmeri resistance. The weak relationship between resistance level and mutation frequency indicates enrichment of additional resistance‐conferring mechanisms. Stronger, contemporary PPO‐inhibitor herbicides are still effective on resistant populations, but rare escapes carry nontarget‐site resistance (NTSR) mechanisms which should be mitigated with other management tools. © 2026 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Keywords: genotyping, molecular assay, nontarget‐site resistance; NTSR; PPO‐inhibitor resistance; target‐site resistance; target‐site mutation accumulation


Over a decade, Arkansas Amaranthus palmeri populations maintained resistance to PPO‐inhibiting herbicides. PPO2 mutations relate to shifts in herbicide resistance patterns over time.

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1. INTRODUCTION

Palmer amaranth (Amaranthus palmeri) is the most problematic weed in US agriculture. It can reduce yields of maize, soybean, and cotton by up to 91%, 68%, and 59%, respectively. 1 , 2 , 3 Since the first documented case of herbicide resistance in A. palmeri in 1989 to trifluralin, this species has subsequently evolved resistance to nine modes of action (MOAs), 4 severely limiting control options. Herbicide resistance evolves through two broad categories of mechanisms: target‐site (TS) and non‐target‐site resistance. The widespread resistance of A. palmeri to glyphosate (Group 9) and acetolactate synthase (ALS) inhibitors has intensified reliance on alternative modes of action, among which are protoporphyrinogen IX oxidase (PPO) inhibitors. Intensive use of PPO‐inhibiting herbicides has, in turn, selected for multiple resistance to this herbicide MOA, threatening the utility of Group 14 herbicides for weed management.

PPO is a membrane‐associated enzyme that catalyzes the oxidation of protoporphyrinogen IX to protoporphyrin IX, the final shared precursor in the biosynthesis of both heme and chlorophyll. 5 In plants, two isoforms are encoded by distinct nuclear genes: PPO1, which is targeted to chloroplasts, and PPO2, which is localized primarily in mitochondria, although in some species, including A. palmeri, PPO2 can be dual‐targeted. 6 , 7 , 8 It is therefore suggested that the PPO2 gene provides a more evolutionarily advantageous path for the evolution of resistance, as PPO2 was previously reported to localize to both chloroplasts and mitochondria in species such as Spinacia oleracea, Amaranthus tuberculatus, and A. palmeri. 8 , 9 However, recent research has demonstrated that both PPO1 and PPO2 are primarily localized in chloroplasts in Arabidopsis, Spinacia, and Amaranthus species. 10 , 11 A vital step in tetrapyrrole biosynthesis is catalyzed by PPO; inhibition of this step leads to the accumulation of photoreactive intermediates and subsequent membrane damage, which underpins the herbicidal activity of PPO‐inhibiting compounds. 12

Commercial PPO inhibitors include several chemical classes, such as diphenyl ethers, N‐phenyl‐imides, N‐phenyl‐oxadiazolones, and N‐phenyl‐triazolinones. Their popularity is driven by high efficacy, broad‐spectrum activity, and residual control, particularly in production systems where resistance to glyphosate and ALS inhibitors is widespread. 13 Differences in weed control performance among PPO inhibitors reflect how their distinct chemical scaffolds mimic the natural substrate and interact with the PPO catalytic site.

Target‐site resistance in PPO2 has been linked to several amino acid changes that alter the inhibitor‐ and/or substrate‐binding environment. The glycine deletion at position 210 (ΔG210) was the first mutation reported and remains the most prevalent resistance allele in A. tuberculatus and A. palmeri. 7 , 14 Structural and functional analyses indicated that ΔG210 enlarges the binding pocket, permitting simultaneous occupancy by inhibitor and substrate while largely preserving substrate binding, which minimizes associated fitness penalties. 15 Other substitutions are not as benign. The G399A substitution, for example, introduces steric hindrance within the binding site and is associated with a substantial reduction in PPO2 catalytic activity. Additional substitutions at R128, a residue critical for substrate binding via ionic interaction with protophyrinogen IX's carboxyl group, have been described in A. tuberculatus, A. palmeri, and A. retroflexus, 16 , 17 , 18 with multiple amino acid replacements reported at this position (R128G, R128I, R128K, R128M). The significance of R128 in protogen binding is due to the establishment of a salt bridge between the positively charged arginine side chain and the negatively charged carboxyl group of ring C of protogen. 19 , 20 , 21

Given the extensive use of PPO‐inhibiting herbicides, the potential for combinations of resistance mutations to arise in the same allele, plant, or population becomes an important question for resistance‐risk assessment. Double‐mutation genotypes involving ΔG210, G399A, and R128 substitutions have been predicted to confer high levels of resistance but could also compromise enzyme function to the point of inviability. Previous studies have shown that when two substitutions (ΔG210 + G399A or ΔG210 + R128) occur on the same allele, the resulting enzyme exhibits little or no catalytic activity due to structural perturbations at the catalytic site. 22 The combined alterations are predicted to substantially modify the active‐site conformation, impairing substrate binding and catalytic turnover. 22 In contrast, when either mutation occurs alone, the enzyme remains catalytically functional and confers partial herbicide resistance. 23 Consistent with these reports, the genotype carrying one double‐mutant allele and one single‐mutant allele is expected to behave functionally as a heterozygote. In this configuration, resistance is primarily conferred by the single‐mutant allele, while the double‐mutant allele contributes little to enzymatic activity due to the structural incompatibility of the combined mutations. These findings highlight the critical role of allelic configuration in determining resistance outcomes.

This research investigated how PPO target‐site resistance and sensitivity to PPO‐inhibiting herbicides have changed over roughly a decade in A. palmeri populations from Greene (GRE‐A) and Crittenden (CRI‐D) counties, Arkansas, USA. These counties have a combined 500K hectares of agricultural land with multiple crops using Group 14 herbicides each year. 24

The specific objectives were to (1) characterize shifts in population‐level resistance to foliar‐ and soil‐applied PPO‐inhibiting herbicides and (2) characterize the dynamics of PPO2 target‐site mutation frequencies in historical vs contemporary populations from the same fields.

2. MATERIALS AND METHODS

2.1. Plant materials and treatment conditions

PPO‐resistant A. palmeri seeds were collected from fields of GRE‐A and CRI‐D counties, Arkansas, USA, between 2015 and 2023. The sampling procedure followed that of Salas et al., 25 collecting the inflorescence of 10 randomly distributed female plants to obtain one composite sample per field. Being dioecious, and consequently an obligate outcrossing species, this number is substantial to represent the field population. Population names were assigned based on seed collection year and field location. In 2015 and 2022, 15‐CRI‐D and 22‐CRI‐D were taken from the same CRI‐D field, whereas 15‐GRE‐A and 23‐GRE‐A were collected in 2015 and 2023 from GRE‐A field. The susceptible (S) reference population was from Crawford County, Arkansas. Seeds were sown in trays (22.9 × 16.5 × 6.4 cm), and two‐leaf stage seedlings were transplanted into 50‐cellular trays, filled with a commercial potting mix (Pro‐Mix; Premier Tech Horticulture, Canada), with one seedling per cell. Plants were grown in a greenhouse maintained at 32/28 °C day/night temperature and a 14‐h photoperiod. Plants were watered as needed and fertilized once weekly (Miracle‐Gro, 15–30‐15 NPK). Herbicides were applied at 187 L ha−1 spray volume using a benchtop sprayer equipped with two flat fan nozzles (110.0067) spaced 50 cm apart and positioned 45 cm above the plant canopy.

2.2. Response to soil‐applied PPO inhibitors

A. palmeri seeds (100 per population) were sown in 22.9 × 16.5 × 6.4 cm trays filled with 1.3 kg of silt‐loam soil that had not been treated with herbicides in more than 20 years. Two pre‐emergence herbicides (fomesafen and sulfentrazone, both at 280 g ai ha−1) were evaluated in a randomized complete block design with three replications. The experiment was conducted twice. Herbicides were applied immediately after planting and activated with mist irrigation. Seedling emergence was assessed 21 days after treatment (DAT) and expressed as a percentage reduction in germination relative to non‐treated checks. Data were analyzed using two‐way analysis of variance (ANOVA) in RStudio Pro 2024.

2.3. Response to foliar‐applied PPO inhibitors

Three PPO‐inhibiting herbicides were tested: saflufenacil (BASF Corp., Research Triangle Park, NC, USA) (25 g ai ha−1), fomesafen (Syngenta Crop Protection, Greensboro, NC, USA) (560 g ai ha−1), and flumioxazin (Valent USA LLC, Irvine, CA, USA) (71 g ai ha−1). The experimental units were arranged in a randomized complete block design with three replications. The experiment was conducted twice. Each replication consisted of a single 50‐cellular tray (28 × 54 cm), filled with commercial potting mix (Pro‐Mix; Premier Tech Horticulture, Canada), with one seedling established per cell. Herbicides were applied when A. palmeri seedlings were between 5‐ and 8‐cm tall. Ammonium‐sulfate was added at 10 g L−1 as an adjuvant. Each experiment included nontreated checks. Herbicide efficacy was visually assessed at 21 DAT for the entire experimental unit (50‐cell tray) relative to the non‐treated control using a 0–100% scale, where 0 = no visible injury and 100 = dead plants. Data were analyzed using the ANOVA function in RStudio Pro 2024.

2.4. Detection of PPO2 target‐site mutations

A total of 240 survivors from the first run of the foliar tests were genotyped for the presence of resistance‐conferring PPO mutations ΔG210, R128G, G399A, and V361A. DNA was extracted from leaf tissue using the standard CTAB protocol. 26 The survivors were genotyped by pyrosequencing. 23 The potential contribution of the most recently reported resistance‐conferring mutation V361A was evaluated using the procedure described in Rangani et al. 27 PPO1 and PPO2 gene copy numbers were quantified using the same DNA samples used for pyrosequencing. Copy number estimates were normalized to the Actin reference gene, 28 and relative gene copy number was calculated using the 2−ΔΔCt method.

3. RESULTS AND DISCUSSION

3.1. Response to soil‐applied PPO‐inhibiting herbicides

The survival frequency with soil‐applied herbicides differed among populations and increased over time in both CRI‐D and GRE‐A fields (Fig. 1). In the 15‐CRI‐D population, the frequency of survival was minimal, at 5% with fomesafen and 10% with sulfentrazone. This level of survival might not be high enough to classify the population as resistant but is a clear indicator of evolving resistance. Prior to the confirmation of field‐level resistance of A. palmeri in Arkansas to fomesafen in 2015, 14 the first cohort of fomesafen‐resistant individuals (ΔG210 mutants) was detected in a sample collected in 2011 with 5% survivors. 25 In the contemporary population (22‐CRI‐D), the survival frequency minimally increased to 7% and 15% with fomesafen and sulfentrazone, respectively. In contrast, the GRE‐A population showed a significant (P = 0.0007) increase in resistance to soil‐applied Group 14 herbicides between 2015 and 2023. Survival from fomesafen and sulfentrazone treatments was 13% and 8%, respectively, in 15‐GRE‐A. This increased considerably to nearly 30% with fomesafen and 16% with sulfentrazone in the contemporary population 23‐GRE‐A. Between the CRI‐D and GRE‐A fields, the historical and contemporary GRE‐A populations consistently had higher resistance to Group 14 herbicides than the CRI‐D populations. Location‐specific differences in resistance patterns could be attributed to two major factors. One is the difference in genomic background of populations. Another is the difference in herbicide use history between fields. The population in GRE‐A field has been exposed to prolonged, intense selection pressure with Group 14 herbicides (fomesafen, acifluorfen, lactofen) to control A. palmeri and other weeds in the commercial production of certified non‐GMO seeds of soybean and rice (personal communication with grower). The CRI‐D field has been historically planted with RoundupReady® or Liberty Link® crops, relying on non‐selective herbicides (glyphosate or glufosinate‐ammonium) and mixtures with other herbicide modes of action to control weeds.

Figure 1.

Figure 1

Survival (%) of Palmer amaranth populations treated with pre‐emergence PPO‐inhibiting herbicides (fomesafen and sulfentrazone at 280 g ai ha−1), evaluated at 3 weeks after treatment (WAT). Bars represent mean survival for fomesafen (pink) and sulfentrazone (blue); error bars indicate the standard deviation of three replicates.

Higher resistance to fomesafen and susceptibility to the other Group 14 herbicides tested aligned with previous research reporting that soil‐applied PPO inhibitors such as saflufenacil, sulfentrazone, and flumioxazin are generally effective on fomesafen‐resistant A. palmeri. 28 , 29 The variability in resistance pattern between the GRE‐A and CRI‐D populations suggests divergent resistance mechanisms, potentially involving different TS mutation profiles and/or different physiological adaptations.

3.2. Response to foliar‐applied PPO‐inhibiting herbicides

The evolution of resistance to foliar‐applied PPO‐inhibiting herbicides in A. palmeri showed distinct trajectories between the GRE‐A and CRI‐D sites, also indicative of divergent herbicide use histories and genomic backgrounds. Across the three herbicide treatments (saflufenacil, fomesafen, and flumioxazin), GRE‐A populations consistently exhibited higher resistance (62–76% injury) compared to CRI‐D populations (>90% injury) (Table 1), suggesting that the population in GRE‐A field has undergone stronger or more prolonged selection for PPO resistance as discussed in section 3.1. In addition, there is an indication of cumulative multiple resistance‐conferring mechanisms within the GRE‐A population. Despite this overall divergence, both historical and recent populations from GRE‐A and CRI‐D responded similarly to foliar‐applied flumioxazin and saflufenacil, indicating that the efficacy of these active ingredients has been sustained during this period. This stability may reflect inherent chemical properties of these herbicides that limit cross‐resistance evolution.

Table 1.

Visible injury (%) at 3 weeks after treatment in Amaranthus palmeri populations from Arkansas, USA treated with foliar‐applied PPO‐inhibiting herbicides.

Visible injury (%)
Population Flumioxazin Fomesafen Saflufenacil
15‐CRI‐D 94ns 91ns 93ns
22‐CRI‐D 92ns 48* 95ns
15‐GRE‐A 62* 68* 67*
23‐GRE‐A 72* 62* 76*
SS 100 100 100
*

Mean values are significantly different from the susceptible standard (SS) at P < 0.05. ns, not significantly different from SS.

Temporal comparisons revealed a marked increase in resistance to fomesafen in the CRI‐D population, which shifted from being susceptible in 2015 (91% control) to high resistance in 2022 (48% control) (Table 1). Conversely, resistance to fomesafen in GRE‐A remained at the 60th percentile in this period (68% control in 2015 and 62% control in 2023). The higher resistance in 15‐GRE‐A vs 15‐CRI‐D to foliar‐applied fomesafen could be attributed to the extensive historical use of fomesafen in the non‐GMO soybean seed production system of GRE‐A, where this herbicide served as a key tool for broadleaf weed control. By contrast, CRI‐D field, which was historically planted with transgenic soybean, corn, and cotton, relied predominantly on glyphosate and glufosinate for several years, with minimal selection pressure from PPO inhibitors. The subsequent rise in fomesafen resistance in CRI‐D between 2015 and 2022 likely reflects a shift in weed management toward greater reliance on PPO‐inhibitor herbicides following the widespread failure of glyphosate and ALS inhibitors to control resistant A. palmeri populations. This pattern underscores how rapid adaptive evolution can occur once new selection pressures are imposed on previously susceptible populations.

Among the Group 14 herbicides evaluated, saflufenacil consistently provided the highest A. palmeri control across populations, corroborating previous report on efficacy rankings (saflufenacil > flumioxazin > carfentrazone > pyraflufen‐ethyl > fomesafen > fluthiacet‐methyl) 10 and reinforcing prior evidence of its robust field performance. 30 , 31 Collectively, these findings support the universally accepted tenet that cropping practices, ergo herbicide use patterns, drive independent yet convergent resistance evolution pathways and population shifts in weeds such as A. palmeri. The contrasting dynamics between GRE‐A and CRI‐D populations highlight the capacity of this species to rapidly adapt to changing herbicide selection regimes and emphasize the critical importance of diversified, proactive resistance management strategies to mitigate further resistance proliferation.

3.3. Target‐site mutation analysis

The primary mechanism conferring resistance to foliar‐applied PPO‐inhibiting herbicides in A. palmeri is the occurrence of target‐site mutations (TSMs) within the PPO2 gene. To elucidate the molecular basis underlying the differential responses observed between GRE‐A and CRI‐D populations, genotyping of known PPO2 mutations and copy number analysis of PPO2 and PPO1 were performed. No increase in gene copy number was detected in GRE‐A (PPO2: 0.6–2.5; PPO1: 0.7–1.5) and in CRI‐D (PPO2:0.2–3.5; PPO1: 0.5–1.8) populations and copy number variation did not correlate with plant response (Supporting Information, Figs S1 and S2), therefore no further studies were conducted on this aspect. Among the detected PPO2 mutations, ΔG210 was the most prevalent (Supporting Information, Table S1), consistent with previous reports about its widespread occurrence and significant contribution to PPO resistance in A. palmeri. 14 , 32 In 2015, fomesafen survivors from the CRI‐D population predominantly carried the ΔG210 + G128 double‐mutation (75%), while the remaining individuals harbored single mutations of either G128 or ΔG210. In contrast, GRE‐A survivors harbored an equal distribution of ΔG210 single‐mutant and ΔG210 + A399 double‐mutant genotypes. Survivors of flumioxazin treatment of CRI‐D predominantly harbored G128 (45%) and ΔG210 + G128 (35%) mutants, whereas GRE‐A survivors were primarily ΔG210 mutants (80%). Saflufenacil survivors were dominated by single mutants with 90% G128 in CRI‐D‐D and 80% ΔG210 in GRE‐A.

A recently reported PPO mutant, V361A, was detected in two survivors. This mutation was first documented in A. palmeri in 2023 33 and was reported to have minimal or no contribution to resistance. Its potential role in resistance was therefore characterized in vitro using representative herbicides from various PPO‐inhibitor herbicide families (Supporting Information, Table S2). Across all Group 14 herbicides tested, IC₅₀ values (herbicide concentration that inhibits enzyme activity by 50%) for the WT PPO2 were in the low nanomolar range, indicating high intrinsic sensitivity of the enzyme to PPO inhibitors. However, the V361A substitution resulted in herbicide‐specific increases in IC₅₀ values. The V361A mutation in PPO2 significantly reduces diphenylether herbicide sensitivity, with acifluorfen (resistance index, RI = 4.3) being most resistant. Fomesafen and nitrofen showed substantial increases in IC₅₀ values (RI = 3.7 and 2.9, respectively), whereas lactofen was less affected (RI = 1.8). Collectively, results indicate that the V361A mutation in PPO2 significantly reduces sensitivity to diphenylether herbicides while having no effect on N‐phenyltriazolinone and N‐phenylimide inhibition.

Overall, the mutation profiles show that the CRI‐D and GRE‐A populations harbor distinct compositions of functional PPO2 mutations, reflecting independent evolutionary trajectories. The difference in resulting predominant genotypes across populations could be due to inherent differences in genomic background and differential selection pressures imposed on these fields. To further assess how specific target‐site configurations contribute to phenotypic resistance, we examined the association between injury levels of genotyped plants and the frequency of single‐ versus double‐ppo2 target‐site mutations within each population (Fig. 2). A. palmeri is diploid, thus only two alleles are present at the target locus. To examine the combined effect of two herbicide‐resistance‐conferring mutations, we analyzed the frequency of the allele that carried both mutations in cis (double‐mutant allele) and that which harbored only one of the two mutations (trans configuration), among the double‐mutant individuals (Supporting Information, Fig. S3). Previous studies indicate that such cis‐configured alleles may contribute to herbicide resistance; however, normal physiological function in these genotypes is largely sustained by the corresponding single‐mutant allele. 23

Figure 2.

Figure 2

Visible injury and PPO2 mutation frequencies among surviving Amaranthus palmeri plants treated with flumioxazin (71 g ai ha−1), fomesafen (560 g ai ha−1), and saflufenacil (25 g ai ha−1). Boxplots represent the distribution of visible injury (%) of surviving plants within the population. Population includes historical (CRI‐D‐2015 and GRE‐A‐2015) and contemporary (CRI‐D‐2022 and GRE‐A‐2023) collections. Pink and blue dotted lines indicate the frequency of single‐ and double PPO target‐site mutations within each population.

Across herbicides and sampling years, the distribution of PPO2 target‐site mutations revealed clear associations between allele genotype and phenotypic resistance. With flumioxazin and fomesafen treatments, the frequency of single mutants increased in the contemporary population, with a corresponding reduction in double mutants, suggesting that application of these herbicides favors the survival of single mutants, which are less physiologically compromised compared to the double mutants. In contrast, saflufenacil appeared to favor double mutants, as more of these genotypes were detected in the contemporary population. We could surmise that the binding affinity of saflufenacil to these double mutants is relatively weak, allowing for enzyme functionality and survival, whereas saflufenacil binding to the single mutants is strong, thereby removing such genotypes from the population.

Among fomesafen survivors, the double‐mutant frequencies declined considerably in recent populations; 68% in 15‐CRI‐D to 35% in 22‐CRI‐D and 50% in 15‐GRE‐A to 20% in 23‐GRE‐A (Fig. 2). Meanwhile, single mutants such as ΔG210 and G128 became predominant (Fig. 2 and Supporting Information, Table S1). The predominance of single mutants supports previous report of potential fitness cost associated with double mutations. 23 Interestingly, among 15‐CRI‐D fomesafen survivors, most plants carrying double mutations had the mutations located on separate alleles, resulting in two predicted functional PPO2 alleles. In contrast, all of the 15‐GRE‐A survivors carrying double mutations had both mutations on the same PPO2 allele, yielding one predicted nonfunctional allele and one functional allele (Supporting Information, Fig. S2). Thus, these individuals were predicted to rely on partial PPO2 activity. Despite this, injury levels in 15‐GRE‐A were lower than in 15‐CRI‐D, suggesting that additional resistance mechanisms were already present in the GRE‐A population at early stages of selection.

Flumioxazin survivors from the CRI‐D field maintained genotypic diversity between 2015 and 2022 with the appearance of wild‐type individuals in the contemporary population (none in 2015, 20% in 2022). Despite these changes, visible injury among survivors remained high during this period, indicating that the predominance of G128 mutation did not confer substantial resistance to flumioxazin. GRE‐A survivors had an overwhelming dominance of a single ΔG210 mutation, reaching near‐fixation (95%) by 2023, but resistance to flumioxazin remained lower than that to fomesafen. This could be because (1) the selection pressure from flumioxazin was low, and (2) PPO2 TSMs alone do not provide strong resistance to flumioxazin.

Between 2015 and 2023, the composition and prevalence of PPO2 TSMs shifted in ways that have important implications for saflufenacil resistance evolution. Both CRI‐D and GRE‐A fields exhibited a decline in single‐mutation frequencies, from 95% in 2015 to 80% in 2022 in CRI‐D and from 80% in 2015 to 70% in 2023 in GRE‐A. Among the double‐mutant plants, the two mutations of interest occurred on separate alleles in both 2015 populations, allowing each allele to produce a functional PPO2 enzyme but still resulting in high injury. By 2022–2023, however, not only had the frequency of double‐mutant individuals increased in both populations, but the mutations were also found in cis configuration on the same allele, a configuration predicted to produce half a nonfunctional PPO2 enzyme. Because A. palmeri is diploid, allelic configuration is critical for determining functional outcomes of TSM combinations. Double‐mutant alleles in cis are expected to lose PPO2 function due to the disruption of catalytic amino acid residues essential for substrate binding and turnover, whereas alleles harboring single substitutions retain catalytic functionality. With this understanding, saflufenacil‐surviving populations may be enriched for additional resistance‐conferring factors beyond the PPO2 target site, highlighting the multifaceted nature of resistance in these populations. This interplay between mutation type, allelic configuration, and enzymatic integrity explains why single mutations dominate field‐evolved populations while double‐mutant alleles remain transient.

Collectively, these findings demonstrate that the evolution of resistance to PPO‐inhibitors in A. palmeri is shaped not only by the presence of specific TSMs but also by their allelic arrangement, herbicide‐specific selection pressures, and the functional constraints imposed by altered enzyme structure. The contrasting mutation profiles and resistance phenotypes observed between GRE‐A and CRI‐D populations reflect independent evolutionary trajectories driven by location‐specific herbicide‐use history. The predominance of functional single mutations, the limited contribution of double mutants, and the variable expression of resistance across herbicides underscore the complex nature of resistance to PPO inhibitors. Double‐mutant alleles are likely constrained by structural incompatibilities, which restrict their ability to contribute to herbicide resistance and help explain the widespread occurrence of single mutations in field populations. These results highlight the need for integrated management strategies with tools and practices that complement the primary herbicide chemistries to thwart the fixation of additional target‐site and non–target‐site evolutionary pathways for resistance.

4. CONCLUSIONS

A. palmeri resistance to PPO‐inhibitor herbicides is characterized by its dynamic nature, specificity to herbicide chemistry, and influence from population history and genomic background. For compromised chemistries, resistance is higher, and more widespread, to foliar‐applied Group 14 herbicides than to soil‐applied products. Alterations in the type, zygosity, and frequency of PPO2 TSMs correspond closely with resistance or sensitivity patterns, with single‐mutant ΔG210 alleles maintaining a primary role in conferring strong resistance to fomesafen. Conversely, resistance to flumioxazin and saflufenacil is moderate or minimal and involves complex mechanisms. The rarity of double‐mutant genotypes and the increase in frequency of single mutations with time indicate physiological limitations associated with double‐mutant PPO2 alleles. Contemporary PPO‐inhibiting herbicides remain effective against most A. palmeri populations, but rare escapes harbor unique resistance mechanisms.

FUNDING INFORMATION

Funding for this research was provided by the Arkansas Soybean Promotion Board grant # GR023715 University of Arkansas Division of Agriculture (UADA), Agricultural Experiment Station (AES) and by BASF Corp. grant # GR015959 UADA‐AES.

CONFLICT OF INTEREST

Authors affiliated with BASF have contributed to the planning and implementation of research activities. All other authors declare no conflict of interest.

Supporting information

Table S1. Frequency of functional PPO mutations in Palmer amaranth populations.

Table S2. Inhibition of wild‐type (WT) and V361A variant protoporphyrinogen oxidase 2 (PPO2) from Amaranthus palmeri by PPO‐inhibiting herbicides.

Figure S1. Copy number variation (CNV) of PPO1 and PPO2 genes in the GRE Palmer amaranth populations collected in 2015 (15‐GRE‐A) and 2023 (23‐GRE‐A) following treatment with PPO‐inhibiting herbicides. CNV was evaluated after exposure to flumioxazin, saflufenacil, and fomesafen. Flumioxazin‐treated samples correspond to IDs 169–188 (15‐GRE‐A) and 189–208 (23‐GRE‐A), saflufenacil‐treated samples to 1–20 (15‐GRE‐A) and 21–40 (23‐GRE‐A), and fomesafen‐treated samples to 81–100 (15‐GRE‐A) and 101–120 (23‐GRE‐A). CNV values represent relative gene copy number normalized to a reference gene.

Figure S2. Copy number variation (CNV) of PPO1 and PPO2 genes in the CRI Palmer amaranth populations collected in 2015 (15‐CRI‐D) and 2023 (22‐CRI‐D) following treatment with PPO‐inhibiting herbicides. CNV was assessed after exposure to flumioxazin, saflufenacil, and fomesafen. Flumioxazin‐treated samples correspond to IDs 209–228 (15‐CRI‐D) and 229–248 (22‐CRI‐D), saflufenacil‐treated samples to 41–60 (15‐CRI‐D) and 61–80 (22‐CRI‐D), and fomesafen‐treated samples to 128–148 (15‐CRI‐D) and 149–168 (22‐CRI‐D). CNV values are relative gene copy numbers normalized to a reference gene.

Figure S3. Frequency of PPO target‐site mutations in Palmer amaranth populations following herbicide treatments. Bar graphs show the frequency (%) of functional, non‐functional, and single PPO mutations in four Palmer amaranth populations: 15‐CRI‐D, 22‐CRI‐D, 15‐GRE‐A, and 23‐GRE‐A. The x axis represents the three PPO‐inhibiting herbicides: fomesafen, saflufenacil, and flumioxazin. Bars are colored according to mutation type: functional mutations, non‐functional mutations, and single mutations. The data are the proportion of plants in each population carrying each mutation type after herbicide treatment.

PS-82-10185-s001.docx (117.8KB, docx)

ACKNOWLEDGEMENTS

The authors gratefully acknowledge Juan C. Velasquez and Giovana de Carvalho Silva for their support and contribution to the greenhouse bioassays and the overall execution of this research.

[Correction added on 12 August 2026, after first online publication: The copyright line was changed.]

DATA AVAILABILITY STATEMENT

The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Table S1. Frequency of functional PPO mutations in Palmer amaranth populations.

Table S2. Inhibition of wild‐type (WT) and V361A variant protoporphyrinogen oxidase 2 (PPO2) from Amaranthus palmeri by PPO‐inhibiting herbicides.

Figure S1. Copy number variation (CNV) of PPO1 and PPO2 genes in the GRE Palmer amaranth populations collected in 2015 (15‐GRE‐A) and 2023 (23‐GRE‐A) following treatment with PPO‐inhibiting herbicides. CNV was evaluated after exposure to flumioxazin, saflufenacil, and fomesafen. Flumioxazin‐treated samples correspond to IDs 169–188 (15‐GRE‐A) and 189–208 (23‐GRE‐A), saflufenacil‐treated samples to 1–20 (15‐GRE‐A) and 21–40 (23‐GRE‐A), and fomesafen‐treated samples to 81–100 (15‐GRE‐A) and 101–120 (23‐GRE‐A). CNV values represent relative gene copy number normalized to a reference gene.

Figure S2. Copy number variation (CNV) of PPO1 and PPO2 genes in the CRI Palmer amaranth populations collected in 2015 (15‐CRI‐D) and 2023 (22‐CRI‐D) following treatment with PPO‐inhibiting herbicides. CNV was assessed after exposure to flumioxazin, saflufenacil, and fomesafen. Flumioxazin‐treated samples correspond to IDs 209–228 (15‐CRI‐D) and 229–248 (22‐CRI‐D), saflufenacil‐treated samples to 41–60 (15‐CRI‐D) and 61–80 (22‐CRI‐D), and fomesafen‐treated samples to 128–148 (15‐CRI‐D) and 149–168 (22‐CRI‐D). CNV values are relative gene copy numbers normalized to a reference gene.

Figure S3. Frequency of PPO target‐site mutations in Palmer amaranth populations following herbicide treatments. Bar graphs show the frequency (%) of functional, non‐functional, and single PPO mutations in four Palmer amaranth populations: 15‐CRI‐D, 22‐CRI‐D, 15‐GRE‐A, and 23‐GRE‐A. The x axis represents the three PPO‐inhibiting herbicides: fomesafen, saflufenacil, and flumioxazin. Bars are colored according to mutation type: functional mutations, non‐functional mutations, and single mutations. The data are the proportion of plants in each population carrying each mutation type after herbicide treatment.

PS-82-10185-s001.docx (117.8KB, docx)

Data Availability Statement

The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions.


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