Background Amaranthus L. is a diverse genus consisting of domesticated, weedy, and non-invasive species distributed around the world. Nine species are dioecious, of which Amaranthus palmeri S. Watson and Amaranthus tuberculatus (Moq.) J.D. Sauer are troublesome weeds of agronomic crops in the USA and elsewhere. Shallow relationships among the dioecious Amaranthus species and the conservation of candidate genes within previously identified A. palmeri and A. tuberculatus male-specific regions of the Y (MSYs) in other dioecious species are poorly understood. In this study, seven genomes of dioecious amaranths were obtained by paired-end short-read sequencing and combined with short reads of seventeen species in the family Amaranthaceae from NCBI database. The species were phylogenomically analyzed to understand their relatedness. Genome characteristics for the dioecious species were evaluated and coverage analysis was used to investigate the conservation of sequences within the MSY regions. Results We provide genome size, heterozygosity, and ploidy level inference for seven newly sequenced dioecious Amaranthus species and two additional dioecious species from the NCBI database. We report a pattern of transposable element proliferation in the species, in which seven species had more Ty3 elements than copia elements while A. palmeri and A. watsonii had more copia elements than Ty3 elements, similar to the TE pattern in some monoecious amaranths. Using a Mash-based phylogenomic analysis, we accurately recovered taxonomic relationships among the dioecious Amaranthus species that were previously identified based on comparative morphology. Coverage analysis revealed eleven candidate gene models within the A. palmeri MSY region with male-enriched coverages, as well as regions on scaffold 19 with female-enriched coverage, based on A. watsonii read alignments. A previously reported FLOWERING LOCUS T (FT) within A. tuberculatus MSY contig was also found to exhibit male-enriched coverages for three species closely related to A. tuberculatus but not for A. watsonii reads. Additional characterization of the A. palmeri MSY region revealed that 78% of the region is made of repetitive elements, typical of a sex determination region with reduced recombination. Conclusions The results of this study further increase our understanding of the relationships among the dioecious species of the Amaranthus genus as well as revealed genes with potential roles in sex function in the species.

Annual grass weeds reduce profits of wheat farmers in the Pacific Northwest. The very-long-chain fatty acid elongase (VLCFA)-inhibiting herbicides S-metolachlor and dimethenamid-P could expand options for control of annual grasses, but are not registered in wheat due to crop injury. Our studies evaluated a safener, fluxofenim, applied to wheat seed for protection of nineteen soft white winter wheat varieties from S-metolachlor, dimethenamid-P and pyroxasulfone herbicides, investigated the response of six varieties (UI Sparrow, LWW 15-72223, UI Magic CL+, Brundage 96, UI Castle CL+ and UI Palouse CL+) to incremental doses of fluxofenim, established fluxofenim dose required to optimally protect the varieties from VLCFA-inhibiting herbicides, and assessed the impact of fluxofenim dose on glutathione S-transferase (GST) activity in three wheat varieties (UI Sparrow, Brundage 96 and UI Castle CL+). Fluxofenim increased the biomass of four varieties treated with S-metolachlor or dimethenamid-P herbicides and one variety treated with pyroxasulfone. Three varieties showed tolerance to the herbicides regardless of the fluxofenim treatment. Estimated fluxofenim doses resulting in 10% biomass reduction of wheat ranged from 0.55 g ai kg-1 seed to 1.23 g ai kg-1 seed. Fluxofenim doses resulting in 90% increased biomass to S-metolachlor, dimethenamid-P, and pyroxasulfone ranged from 0.07 to 0.55, 0.09 to 0.73, and 0.30 to 1.03 g ai kg-1 seed, respectively. Fluxofenim at 0.36 g ai kg-1 seed increased GST activity in UI Castle CL+, UI Sparrow and Brundage 96 by 58%, 30% and 38%, respectively. These results suggest that fluxofenim would not damage wheat seedlings up to 3x the rate labeled for sorghum, and fluxofenim protects soft white winter wheat varieties from S-metolachlor, dimethenamid-P or pyroxasulfone injury at the herbicide rates evaluated.

Due to the lack of effective POST herbicide options, producers typically rely on nicosulfuron as the main POST grass herbicide in sweet corn production systems. In 2019, a Wisconsin sweet corn producer reported fall panicum control escapes after spraying nicosulfuron. Seeds from mature plants were collected to i) measure fall panicum response to acetolactate synthase [ALS]-inhibiting herbicides, ii) elucidate the resistance mechanism, and iii) evaluate its response to alternative POST herbicides. Greenhouse and laboratory investigations were conducted to assess fall panicum response to ALS-inhibiting herbicides and elucidate the resistance mechanism. Dose-response results showed that fall panicum was highly resistant to nicosulfuron with a resistance ratio of >12.9-fold (survived rates >254 g ai ha−1 or 8X the field label rate). Molecular and genetic studies indicated that there are multiple ALS gene copies in fall panicum and resistance was due to a mutation in one copy, resulting in an Asp-376-Glu amino acid substitution. Additional greenhouse experiments indicate that clethodim (105 g ai ha−1), quizalofop-p-ethyl (70 g ae ha−1), glyphosate (864 g ae ha−1), and glufosinate (650 g ai ha−1) are effective POST options to manage the ALS-resistant fall panicum (>90.0% control and 96.8% biomass reduction) in rotational years. The 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibiting herbicides isoxaflutole (105 g ai ha−1), mesotrione (105 g ai ha−1), tembotrione (92 g ai ha−1), and tolpyralate (39 g ai ha−1) did not provide effective POST fall panicum control. Because these herbicides are commonly used for POST weed control in sweet corn, more investigations are required to evaluate combinations of HPPD-inhibiting herbicides with herbicides from other sites of action for POST fall panicum control. Herein we confirm the first case of herbicide resistance in fall panicum in the United States.

Background The genus Amaranthus L. consists of 70–80 species distributed across temperate and tropical regions of the world. Nine species are dioecious and native to North America; two of which are agronomically important weeds of row crops. The genus has been described as taxonomically challenging and relationships among species including the dioecious ones are poorly understood. In this study, we investigated the phylogenetic relationships among the dioecious amaranths and sought to gain insights into plastid tree incongruence. A total of 19 Amaranthus species’ complete plastomes were analyzed. Among these, seven dioecious Amaranthus plastomes were newly sequenced and assembled, an additional two were assembled from previously published short reads sequences and 10 other plastomes were obtained from a public repository (GenBank). Results Comparative analysis of the dioecious Amaranthus species’ plastomes revealed sizes ranged from 150,011 to 150,735 bp and consisted of 112 unique genes (78 protein-coding genes, 30 transfer RNAs and 4 ribosomal RNAs). Maximum likelihood trees, Bayesian inference trees and splits graphs support the monophyly of subgenera Acnida (7 dioecious species) and Amaranthus; however, the relationship of A. australis and A. cannabinus to the other dioecious species in Acnida could not be established, as it appears a chloroplast capture occurred from the lineage leading to the Acnida + Amaranthus clades. Our results also revealed intraplastome conflict at some tree branches that were in some cases alleviated with the use of whole chloroplast genome alignment, indicating non-coding regions contribute valuable phylogenetic signals toward shallow relationship resolution. Furthermore, we report a very low evolutionary distance between A. palmeri and A. watsonii, indicating that these two species are more genetically related than previously reported. Conclusions Our study provides valuable plastome resources as well as a framework for further evolutionary analyses of the entire Amaranthus genus as more species are sequenced.

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