A quantitative assay for <i>Amaranthus palmeri</i> identification

Murphy, Brent P; Plewa, D.; Phillippi, Elizabeth; Bissonnette, Suzanne M; Tranel, Patrick J.

doi:10.1002/ps.4632

Cited by 18 publications

(17 citation statements)

References 6 publications

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“…At a dilution of 1:81 A. tuberculatus DNA with A. palmeri DNA, the ΔΔcycle threshold value was distinguishable from all other tested species, with the exception of A. arenicola . Previously, the mixed DNA method was demonstrated to be comparable with seed lot extracted DNA samples (Murphy et al, 2017), indicating the developed A. tuberculatus markers can be applied to seed lot screening. Theoretically, the DNA barcode itself could be used as a surveillance tool for bulked population samples.…”

Section: Resultsmentioning

confidence: 99%

“…Since A. arenicola was not present within the reference panel, its behavior at loci believed to be specific for A. tuberculatus cannot be predicted. The SNP 108A, specific to A. palmeri , was previously validated (Murphy et al, 2017).…”

Section: Resultsmentioning

confidence: 99%

“…Previously, a new method for the identification of A. palmeri contamination in mixed seed lots was developed (Murphy et al, 2017) based on polymorphisms in the ITS region, which has proven to be a suitable barcoding region to differentiate Amaranthus spp. (Wetzel et al, 1999a; Waselkov, 2013).…”

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confidence: 99%

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Identification and Validation of Amaranthus Species‐Specific SNPs within the ITS Region: Applications in Quantitative Species Identification

Murphy

Tranel

2018

Crop Science

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The Amaranthus genus consists of as many as 70 species, many with similar morphology. The development and validation of a DNA barcode specific to key amaranths would aid in plant identification. These barcodes can be used to develop assays for single‐species identification, critical for species surveillance and contaminant screening. A reference panel of 75 internal transcribed spacer (ITS) sequences from the National Center for Biotechnology Information (NCBI) across 11 Amaranthus spp. was analyzed for species‐specific single‐nucleotide polymorphisms (SNPs). Identified SNPs were validated using 92 accessions of an Amaranthus spp. diversity panel. Of the 75 investigated ITS sequences from NCBI, 13 were identified as potentially mislabeled. Phylogenetic analysis of ITS from the reference panel distinguished 9 of the 11 investigated species. Nine SNPs were validated as species specific. Five species were distinguished with single SNPs. To illustrate the utility of the ITS SNP analysis, a quantitative assay for Amaranthus tuberculatus (Moq.) Sauer identification was constructed targeting SNP 73G and validated using simulated population samples. Results from this research will aid in population screening for A. tuberculatus, and in the development of other quantitative detection assays for Amaranthus.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Identification and Validation of Amaranthus Species‐Specific SNPs within the ITS Region: Applications in Quantitative Species Identification

Murphy

Tranel

2018

Crop Science

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“…Because these two species are at times difficult to distinguish in the field, it is plausible that these populations contained Palmer amaranth individuals. However, upon use of Palmer amaranth identification primers in RT‐PCR, none of the tested plants with the R128 AGG codon was confirmed to be Palmer amaranth (Fig. b).…”

Section: Resultsmentioning

confidence: 99%

“…The Palmer amaranth PPX2 allele with the R128 AGG codon was found in several populations. To check whether these populations contained Palmer amaranth individuals, RT‐PCR was performed using Palmer amaranth identification primers …”

Section: Methodsmentioning

confidence: 99%

Investigating target‐site resistance mechanism to the PPO‐inhibiting herbicide fomesafen in waterhemp and interspecific hybridization of Amaranthus species using next generation sequencing

Nie

Mansfield

Harre

et al. 2019

Pest Management Science

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BACKGROUND Waterhemp (Amaranthus tuberculatus (Moq.) J. D. Sauer) is one of the most pernicious weeds in cropping systems of the USA due to its evolved resistance against several herbicide sites‐of‐action, including protoporphyrinogen oxidase inhibitors (PPO‐R). Currently, the only source of PPO‐R documented in waterhemp is ΔG210 of PPX2. Gene flow may not only lead to a transfer of herbicide‐resistant alleles, but also produce a hybrid genotype more competitively fit than one or both parents. However, investigating gene flow of Amaranthus species has been of interest in the past two decades with limited evidence. RESULTS Here, a high‐throughput MiSeq amplicon sequencing method was used to investigate alterations of the PPX2 gene in 146 PPO‐R waterhemp populations across five Midwest states of the USA. Five R128 codons of PPX2, novel to waterhemp, were found including AGG (R), GGA (G), GGG (G), AAA (K) and ATA (I). R128G, R128I, and R128K were found in 11, 3, and 2 populations, respectively. R128G and R128I, but not R128K, conferred fomesafen resistance in a bacterial system. Sequence alignment of the R128 region of PPX2 identified a tumble pigweed (Amaranthus albus)‐type and Palmer amaranth (Amaranthus palmeri)‐type PPX2 allele to be present and widespread in the surveyed waterhemp populations, thus providing strong evidence of gene flow between Amaranthus species. CONCLUSION Using a next‐generation sequencing method, we identified two PPO target‐site mutations R128G/I novel to waterhemp and provided evidence of gene flow of Amaranthus species in a large group of screened waterhemp populations from five Midwest states of the USA. © 2019 Society of Chemical Industry

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Comparison of methods to recover amaranth weed seeds from manure

Wilson

Brusa

Christensen

et al. 2022

Agricultural & Env Letters

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One pathway by which Palmer amaranth (Amaranthus palmeri S. Watson) invades new areas is through importation of contaminated livestock feed, which then contaminates land‐applied manure. If contaminated feed is suspected, detection tools are needed to test manure, but traditional methods are time consuming and often inconclusive. Although new genetic seed testing is making detection easier, methods to separate seed from contaminated manure are needed. Six methods were compared for their ability to recover 100 Palmer amaranth seeds added to bedded or nonbedded cattle manure: dry sieving, rinse sieving, manure saturation sieving without blending and with blending, and dispersion sieving without blending and with blending. Seed recovery was highest (>90%) with the rinse sieving method regardless of manure type. The dispersion methods are not recommended as they recovered <24.7% of seeds. Following each method, genetic testing successfully identified Palmer amaranth presence, indicating no interference of recovery method with DNA extraction.

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A quantitative assay for Amaranthus palmeri identification

Abstract: A qPCR assay for distinguishing A. palmeri from 12 other Amaranthus spp. was developed and validated. The assay can consistently detect a single A. palmeri seed when present in a pool of 100 total Amaranthus spp. seeds. © 2017 Society of Chemical Industry.

Cited by 18 publications

References 6 publications

Identification and Validation of Amaranthus Species‐Specific SNPs within the ITS Region: Applications in Quantitative Species Identification

Identification and Validation of Amaranthus Species‐Specific SNPs within the ITS Region: Applications in Quantitative Species Identification

Investigating target‐site resistance mechanism to the PPO‐inhibiting herbicide fomesafen in waterhemp and interspecific hybridization of Amaranthus species using next generation sequencing

Comparison of methods to recover amaranth weed seeds from manure

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