Mutations conferring evolved herbicide resistance in weeds are known in nine different herbicide sites of action. This review summarizes recently reported resistance-conferring mutations for each of these nine target sites. One emerging trend is an increase in reports of multiple mutations, including multiple amino acid changes at the glyphosate target site, as well as mutations involving two nucleotide changes at a single amino acid codon. Standard reference sequences are suggested for target sites for which standards do not already exist. We also discuss experimental approaches for investigating cross-resistance patterns and for investigating fitness costs of specific target-site mutations.

Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri are agronomically important weed species. Here, we present the most contiguous draft assemblies of these three species to date. We utilized a combination of Pacific Biosciences long-read sequencing and chromatin contact mapping information to assemble and order sequences of A. palmeri to near-chromosome-level resolution, with scaffold N50 of 20.1 Mb. To resolve the issues of heterozygosity and co-assembly of alleles in diploid species, we adapted the trio binning approach to produce haplotype assemblies of A. tuberculatus and A. hybridus. This approach resulted in an improved assembly of A. tuberculatus, and the first genome assembly for A. hybridus, with contig N50s of 2.58 and 2.26 Mb, respectively. Species-specific transcriptomes and information from related species were used to predict transcripts within each assembly. Syntenic comparisons of these species and Amaranthus hypochondriacus identified sites of genomic rearrangement, including duplication and translocation, while genetic map construction within A. tuberculatus highlighted the need for further ordering of the A. hybridus and A. tuberculatus contigs. These multiple reference genomes will accelerate genomic studies in these species to further our understanding of weedy evolution within Amaranthus.

Herbicide resistance within key driver weeds, such as common waterhemp [Amaranthus tuberculatus (Moq.) Sauer var. rudis (Sauer) Costea and Tardif ], constrains available management options for crop production. Routine surveillance for herbicide resistance provides a mechanism to monitor the development and spread of resistant populations over time. Furthermore, the identification and quantification of resistance mechanisms at the population level can provide information that helps growers develop effective management plans. Populations of Amaranthus spp., including A. tuberculatus, redroot pigweed (Amaranthus retroflexus L.), and Palmer amaranth (Amaranthus palmeri S. Watson), were collected from 51 fields in Ohio during the 2016 growing season. Twenty-four A. tuberculatus populations were screened for resistance to the herbicides lactofen, atrazine, and glyphosate. Phenotypically resistant plants were further investigated to determine the frequency of known resistance mechanisms. Resistance to lactofen was infrequently observed throughout the populations, with 8 of 22 populations exhibiting resistant plants. Within those eight resistant populations, the ΔG210 resistance mechanism was observed in 17 of 30 phenotypically resistant plants, and the remainder lacked all known resistance mechanisms. Resistance to atrazine was observed in 12 of 15 populations; however, a target-site resistance mechanism was not observed in these populations. Resistance to glyphosate was observed in all populations. Gene amplification was the predominant glyphosate-resistance mechanism (147 of 322 plants) in the evaluated populations. The Pro-106-Ser mutation was identified in 24 plants, half of which also possessed gene amplification. In this study, molecular screening generally underestimated the phenotypically observed resistance. Continued mechanism discovery and marker development is required for improved detection of herbicide resistance through molecular assays.

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.

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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Main conclusion Amplification and overexpression of the target site glutamine synthetase, specifically the plastid-located isoform, confers resistance to glufosinate in Amaranthus palmeri. This mechanism is novel among glufosinate-resistant weeds. Abstract Amaranthus palmeri has recently evolved resistance to glufosinate herbicide. Several A. palmeri populations from Missouri and Mississippi, U.S.A. had survivors when sprayed with glufosinate-ammonium (GFA, 657 g ha−1). One population, MO#2 (fourfold resistant) and its progeny (sixfold resistant), were used to study the resistance mechanism, focusing on the herbicide target glutamine synthetase (GS). We identified four GS genes in A. palmeri; three were transcribed: one coding for the plastidic protein (GS2) and two coding for cytoplasmic isoforms (GS1.1 and GS1.2). These isoforms did not contain mutations associated with resistance. The 17 glufosinate survivors studied showed up to 21-fold increase in GS2 copies. GS2 was expressed up to 190-fold among glufosinate survivors. GS1.1 was overexpressed > twofold in only 3 of 17, and GS1.2 in 2 of 17 survivors. GS inhibition by GFA causes ammonia accumulation in susceptible plants. Ammonia level was analyzed in 12 F1 plants. GS2 expression was negatively correlated with ammonia level (r =  – 0.712); therefore, plants with higher GS2 expression are less sensitive to GFA. The operating efficiency of photosystem II (ϕPSII) of Nicotiana benthamiana overexpressing GS2 was four times less inhibited by GFA compared to control plants. Therefore, increased copy and overexpression of GS2 confer resistance to GFA in A. palmeri (or other plants). We present novel understanding of the role of GS2 in resistance evolution to glufosinate.

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