Genetic architecture underlying HPPD ‐inhibitor resistance in a Nebraska Amaranthus tuberculatus population

Genetic architecture underlying HPPD-inhibitor resistance in a Nebraska Amaranthus tuberculatus population

10.1101/2021.06.11.448079 ◽

2021 ◽

Author(s):

Brent P Murphy ◽

Roland Beffa ◽

Patrick J Tranel

Keyword(s):

Weed Management ◽

Genetic Architecture ◽

Cropping Systems ◽

Dominant Trait ◽

Weed Species ◽

Primary Driver ◽

Amaranthus Tuberculatus ◽

Resistance Trait ◽

F2 Generation ◽

Inhibitor Resistance

BACKGROUND: Amaranthus tuberculatus is a primary driver weed species throughout the American Midwest. Inhibitors of 4-hydroxyphenylpyruvate dioxygenase (HPPD) are an important chemistry for weed management in numerous cropping systems. Here, we characterize the genetic architecture underlying the HPPD-inhibitor resistance trait in an A. tuberculatus population (NEB). RESULTS: Dose-response studies of an F1 generation identified HPPD-inhibitor resistance as a dominant trait with a resistance/sensitive ratio of 15.0-21.1. Segregation analysis in a pseudo-F2 generation determined the trait is moderately heritable (H2 = 0.556), and complex. Bulk segregant analysis and validation with molecular markers identified two quantitative trait loci (QTL), one on each of Scaffold 4 and 12. CONCLUSIONS: Resistance to HPPD-inhibitors is a complex, largely dominant trait within the NEB population. Two large-effect QTL were identified controlling HPPD-inhibitor resistance in A. tuberculatus. This is the first QTL mapping study to characterize herbicide resistance in a weedy species.

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Nontarget-Site Resistance to ALS Inhibitors in Waterhemp (Amaranthus tuberculatus)

Weed Science ◽

10.1614/ws-d-14-00139.1 ◽

2015 ◽

Vol 63 (2) ◽

pp. 399-407 ◽

Cited By ~ 31

Author(s):

Jiaqi Guo ◽

Chance W. Riggins ◽

Nicholas E. Hausman ◽

Aaron G. Hager ◽

Dean E. Riechers ◽

...

Keyword(s):

Acetolactate Synthase ◽

Enzyme Assays ◽

Whole Plant ◽

Site Of Action ◽

Amaranthus Tuberculatus ◽

Resistance Trait ◽

Als Inhibitors ◽

Moderate Resistance ◽

Inhibitor Resistance ◽

Als Inhibitor

A waterhemp population (MCR) previously characterized as resistant to 4-hydroxyphenylpyruvate dioxygenase and photosystem II inhibitors demonstrated both moderate and high levels of resistance to acetolactate synthase (ALS) inhibitors. Plants from the MCR population exhibiting high resistance to ALS inhibitors contained the commonly found Trp574Leu ALS amino acid substitution, whereas plants with only moderate resistance did not have this substitution. A subpopulation (JG11) was derived from the MCR population in which the moderate-resistance trait was isolated from the Trp574Leu mutation. Results from DNA sequencing and ALS enzyme assays demonstrated that resistance to ALS inhibitors in the JG11 population was not due to an altered site of action. This nontarget-site ALS-inhibitor resistance was characterized with whole-plant dose–response experiments using herbicides from each of the five commercialized families of ALS-inhibiting herbicides. Resistance ratios ranging from 3 to 90 were obtained from the seven herbicides evaluated. Nontarget-site resistance to ALS has been rarely documented in eudicot weeds, and adds to the growing list of resistance traits evolved in waterhemp.

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Comparing responses of sensitive and resistant populations of Palmer amaranth (Amaranthus palmeri) and waterhemp (Amaranthus tuberculatus var. rudis) to PPO inhibitors

Weed Technology ◽

10.1017/wet.2019.84 ◽

2019 ◽

Vol 34 (1) ◽

pp. 140-146 ◽

Cited By ~ 4

Author(s):

Kathryn J. Lillie ◽

Darci A. Giacomini ◽

Patrick J. Tranel

Keyword(s):

Palmer Amaranth ◽

Amaranthus Palmeri ◽

Resistant Population ◽

Evolution Of Resistance ◽

Amaranthus Tuberculatus ◽

Inhibitor Resistance ◽

Dose Responses ◽

Sensitive Population ◽

Respective Species ◽

Better Than

AbstractResistance to protoporphyrinogen oxidase (PPO) inhibitors was first observed in waterhemp in 2001 and was conferred by the deletion of a glycine residue at the 210th position (ΔGly-210) of the PPO enzyme. PPO-inhibitor resistance in Palmer amaranth was first observed in 2011, 10 years later. The objectives of this study were to directly compare PPO inhibitor responses in plants of both species with or without the ΔGly-210 mutation. Using greenhouse experiments, early (EPOST) and late (LPOST) postemergence dose responses using lactofen and fomesafen, and preemergence (PRE) dose responses using fomesafen and flumioxazin, were obtained for a sensitive and resistant population each of waterhemp and Palmer amaranth. An additional spray study confirmed each sensitive population used in the dose responses was representative of its respective species, with regards to PPO-inhibitor sensitivity. When treated at either POST timing, Palmer amaranth was more tolerant than waterhemp, and the ΔGly-210 mutation provided greater resistance in Palmer amaranth (48-fold to >3,440-fold, depending on timing and herbicide) than in waterhemp (31-fold to 123-fold). The level of tolerance in Palmer amaranth was striking; the sensitive Palmer amaranth population treated LPOST survived as well or better than the resistant waterhemp population treated EPOST. With PRE applications, response differences both between species and between resistant and sensitive populations generally were less pronounced, relative to POST applications. Collectively, this research indicates Palmer amaranth tolerance to POST-applied PPO inhibitors could have initially slowed (relative to waterhemp) evolution of resistance to these herbicides, and resistant and sensitive populations of both species are more likely to be effectively controlled with PRE rather than POST applications.

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The genetic architecture and genome‐wide signatures of glyphosate resistance in Amaranthus tuberculatus

Molecular Ecology ◽

10.1111/mec.15920 ◽

2021 ◽

Author(s):

J.M. Kreiner ◽

P.J. Tranel ◽

D. Weigel ◽

J.R. Stinchcombe ◽

S.I. Wright

Keyword(s):

Genetic Architecture ◽

Glyphosate Resistance ◽

Genome Wide ◽

Amaranthus Tuberculatus

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Distribution of the ΔG210 Protoporphyrinogen Oxidase Mutation in Illinois Waterhemp (Amaranthus tuberculatus) and an Improved Molecular Method for Detection

Weed Science ◽

10.1614/ws-d-15-00037.1 ◽

2015 ◽

Vol 63 (4) ◽

pp. 839-845 ◽

Cited By ~ 12

Author(s):

R. Joseph Wuerffel ◽

Julie M. Young ◽

Ryan M. Lee ◽

Patrick J. Tranel ◽

David A. Lightfoot ◽

...

Keyword(s):

Amino Acid Position ◽

Molecular Method ◽

Site Mutation ◽

Protoporphyrinogen Oxidase ◽

Phenotypic Resistance ◽

Detection Techniques ◽

Specific Pcr ◽

Allele Specific ◽

Amaranthus Tuberculatus ◽

Inhibitor Resistance

Molecular assays are often implemented by weed scientists for detection of herbicide-resistant individuals; however, the utility of these assays can be limited if multiple mechanisms of evolved resistance exist. Waterhemp resistant to protoporphyrinogen oxidase (PPO)– inhibiting herbicides is conferred by a target-site mutation in PPX2L (a gene coding for PPO), resulting in the loss of a glycine at position 210 (ΔG210). This ΔG210 mutation of PPX2L is the only known mechanism responsible for PPO-inhibitor resistance (PPO-R) in waterhemp from five states (Illinois, Indiana, Iowa, Kansas, and Missouri); however, a limited number of populations have been tested, especially in Illinois. To verify the ubiquity of the ΔG210 in PPO-R waterhemp populations in Illinois, a previously published allele-specific PCR (asPCR) was used for the detection of the ΔG210 mutation to associate this mutation with phenotypic resistance in 94 Illinois waterhemp populations. The ΔG210 mutation was detected in all populations displaying phenotypic resistance to lactofen (220 g ai ha−1), indicating the deletion is likely the only mechanism of resistance. With evidence that the ΔG210 mutation dominates PPO-R waterhemp biotypes, molecular detection techniques have considerable utility. Unfortunately, the previously published asPCR is time consuming, very sensitive to PCR conditions, and requires additional steps to eliminate the possibility of false negatives. To overcome these limitations, a streamlined molecular method using the TaqMan® technique was developed, utilizing allele-specific, fluorescent probes for high-throughput, robust discrimination of each allele (resistant and susceptible) at the 210th amino acid position of PPX2L.

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Coevolution of resistance to PPO inhibitors in waterhemp (Amaranthus tuberculatus) and Palmer amaranth (Amaranthus palmeri)

Weed Science ◽

10.1017/wsc.2019.41 ◽

2019 ◽

Vol 67 (05) ◽

pp. 521-526 ◽

Cited By ~ 4

Author(s):

Kathryn J. Lillie ◽

Darci A. Giacomini ◽

Jonathan D. Green ◽

Patrick J. Tranel

Keyword(s):

Palmer Amaranth ◽

Amaranthus Palmeri ◽

Pcr Assay ◽

Common Waterhemp ◽

First Case ◽

Amaranthus Tuberculatus ◽

Single Field ◽

Inhibitor Resistance ◽

Amino Acid Glycine ◽

Quantitative Pcr Assay

AbstractThe first case of evolved protoporphyrinogen oxidase (PPO)-inhibitor resistance was observed in 2001 in common waterhemp [Amaranthus tuberculatus (Moq.) Sauer var. rudis (Sauer) Costea and Tardif]. This resistance in A. tuberculatus is most commonly conferred by deletion of the amino acid glycine at the 210th position (ΔGly-210) of the PPO enzyme (PPO2) encoded by PPX2. In a field in Kentucky in 2015, inadequate control of Amaranthus plants was observed following application of a PPO inhibitor. Morphological observations indicated that survivors included both A. tuberculatus and Palmer amaranth (Amaranthus palmeri S. Watson). Research was conducted to confirm species identities and resistance and then to determine whether resistance evolved independently in the two species or via hybridization. Results from a quantitative PCR assay based on the ribosomal internal transcribed spacer confirmed that both A. tuberculatus and A. palmeri coexisted in the field. The mutation conferring ΔGly-210 in PPO2 was identified in both species; phylogenetic analysis of a region of PPX2, however, indicated that the mutation evolved independently in the two species. Genotyping of greenhouse-grown plants that survived lactofen indicated that all A. tuberculatus survivors, but only a third of A. palmeri survivors, contained the ΔGly-210 mutation. Consequently, A. palmeri plants were evaluated for the presence of an arginine to glycine or methionine substitution at position 128 of PPO2 (Arg-128-Gly and Arg-128-Met). The Arg-128-Gly substitution was found to account for resistance that was not accounted for by the ΔGly-210 mutation in plants from the A. palmeri population. Results from this study provide a modern-day example of both parallel and convergent evolution occurring within a single field.

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