Development of a rapid detection assay for acetolactate synthase inhibitors resistance in three Amaranthus weed species through loop-mediated isothermal amplification

BACKGROUND

The early detection of herbicide resistance in weeds is a key factor to avoid herbicide waste and improve agriculture sustainability. The present study aimed to develop and validate an allele-specific loop-mediated isothermal amplification (AS-LAMP) assay for the quick on-site detection of the resistance-endowing point mutation Trp-574-Leu in the acetolactate synthase (ALS) gene in three widely diffused Amaranthus weed species: Amaranthus retroflexus, Amaranthus hybridus and Amaranthus tuberculatus.

RESULTS

The AS-LAMP protocol was developed on wild-type and ALS-mutant plants of the three species and revealed that the amplification approach with only the primer set specific for the mutant allele (574-Leu) was the most promising. The validation and estimation of the AS-LAMP performance evaluated by comparing the results with those of the molecular marker (cleaved amplified polymorphic sequences) indicated that, although the sensitivity and specificity were relatively high in all species (overall 100 and > 65%, respectively), precision was high for A. hybridus L. and A. retroflexus L. (75 and 79%, respectively), but quite low for A. tuberculatus (Moq.) J. D. Sauer (59%). The LAMP assay was also effective on crude genomic DNA extraction, allowing the quick detection of mutant plants in field situation (on site resistance detection).

CONCLUSION

The proposed AS-LAMP method has proven to be a promising technique for rapid detection of resistance as a result of Trp-574-Leu on the two monoecious weedy Amaranthus species but resulted less effective in the genetically variable dioecious species A. tuberculatus. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Fagopyrum esculentum Alters Its Root Exudation after Amaranthus retroflexus Recognition and Suppresses Weed Growth

Weed control by crops through growth suppressive root exudates is a promising alternative to herbicides. Buckwheat (Fagopyrum esculentum) is known for its weed suppression and redroot pigweed (Amaranthus retroflexus) control is probably partly due to allelopathic root exudates. This work studies whether other weeds are also suppressed by buckwheat and if the presence of weeds is necessary to induce growth repression. Buckwheat and different weeds were co-cultivated in soil, separating roots by a mesh allowing to study effects due to diffusion. Buckwheat suppressed growth of pigweed, goosefoot and barnyard grass by 53, 42, and 77% respectively without physical root interactions, probably through allelopathic compounds. Root exudates were obtained from sand cultures of buckwheat (BK), pigweed (P), and a buckwheat/pigweed mixed culture (BK-P). BK-P root exudates inhibited pigweed root growth by 49%. Characterization of root exudates by UHPLC-HRMS and principal component analysis revealed that BK and BK-P had a different metabolic profile suggesting that buckwheat changes its root exudation in the presence of pigweed indicating heterospecific recognition. Among the 15 different markers, which were more abundant in BK-P, tryptophan was identified and four others were tentatively identified. Our findings might contribute to the selection of crops with weed suppressive effects.

The complete chloroplast genome sequences for four Amaranthus species (Amaranthaceae)

PREMISE OF THE STUDY

The amaranth genus contains many important grain and weedy species. We further our understanding of the genus through the development of a complete reference chloroplast genome.

METHODS AND RESULTS

A high-quality Amaranthus hypochondriacus (Amaranthaceae) chloroplast genome assembly was developed using long-read technology. This reference genome was used to reconstruct the chloroplast genomes for two closely related grain species (A. cruentus and A. caudatus) and their putative progenitor (A. hybridus). The reference genome was 150,518 bp and possesses a circular structure of two inverted repeats (24,352 bp) separated by small (17,941 bp) and large (83,873 bp) single-copy regions; it encodes 111 genes, 72 for proteins. Relative to the reference chloroplast genome, an average of 210 single-nucleotide polymorphisms (SNPs) and 122 insertion/deletion polymorphisms (indels) were identified across the analyzed genomes.

CONCLUSIONS

This reference chloroplast genome, along with the reported simple sequence repeats, SNPs, and indels, is an invaluable genetic resource for studying the phylogeny and genetic diversity within the amaranth genus.

The complete chloroplast genome sequences for four Amaranthus species (Amaranthaceae)

PREMISE OF THE STUDY

The amaranth genus contains many important grain and weedy species. We further our understanding of the genus through the development of a complete reference chloroplast genome.

METHODS AND RESULTS

A high-quality Amaranthus hypochondriacus (Amaranthaceae) chloroplast genome assembly was developed using long-read technology. This reference genome was used to reconstruct the chloroplast genomes for two closely related grain species (A. cruentus and A. caudatus) and their putative progenitor (A. hybridus). The reference genome was 150,518 bp and possesses a circular structure of two inverted repeats (24,352 bp) separated by small (17,941 bp) and large (83,873 bp) single-copy regions; it encodes 111 genes, 72 for proteins. Relative to the reference chloroplast genome, an average of 210 single-nucleotide polymorphisms (SNPs) and 122 insertion/deletion polymorphisms (indels) were identified across the analyzed genomes.

CONCLUSIONS

This reference chloroplast genome, along with the reported simple sequence repeats, SNPs, and indels, is an invaluable genetic resource for studying the phylogeny and genetic diversity within the amaranth genus.

Influence of Epidemiological Factors on the Bioherbicidal Efficacy of Phomopsis amaranthicola on Amaranthus hybridus

Greenhouse experiments were performed to determine the effect of dew period temperature and duration, plant growth stage, conidial concentration, and the addition of adjuvants on the bioherbicidal efficacy of Phomopsis amaranthicola on Amaranthus spp., using Amaranthus hybridus as test plant. P. amaranthicola infected A. hybridus at 20, 25, 30, and 35°C but the disease level achieved at 20°C may not be sufficient to cause high plant mortality. Plant mortality was also significantly lower in plants that were exposed to 4 h of dew. Plants at less than two- to two- to four-leaf stage were more easily killed than older plants, and increasing conidial concentration from 10⁵ to 10⁶ or 10⁷ conidia ml^-1 did not result in higher mortality levels. Among the adjuvants tested, polyalkyleneoxide-modified heptamethyltrisiloxane, algal polysaccharide, hyrdroxyethyl cellulose, and octylphenoxy polyethoxyethanol reduced conidial germination. Conidia applied with invert emulsion caused the highest plant mortality (74%) but invert emulsion alone caused 33% plant death due to phytotoxicity. Results indicate that P. amaranthicola can infect and kill Amaranthus spp. under a range of temperature, dew period, and inoculum levels and, therefore, has good potential as a bioherbicide agent.

Field Evaluation of Phomopsis amaranthicola, A Biological Control Agent of Amaranthus spp

There are approximately 60 species in the genus Amaranthus, of which seven are used as grains, leafy vegetables, or ornamentals. The majority of the remaining species are considered important weeds. A new fungal species, Phomopsis amaranthicola, isolated from stem and leaf lesions on an Amaranthus sp. plant, was found to be pathogenic to 22 species of Amaranthus tested. The efficacy of this fungus was tested in field trials using one or two postemergent applications of the fungus consisting of two concentrations of conidia or mycelial suspensions. Species tested for susceptibility in the field included Amaranthus hybridus, A. lividus, A. viridus, A. spinosus, and a triazine-resistant A. hybridus. The cumulative disease incidence data for each treatment within each species were plotted versus time using regression for lifetime data. Plant mortality was recorded 2, 4, and 6 weeks after inoculation. There were significant differences between the treatment effects in the control plots versus the plots treated with P. amaranthicola. The highest level of control was obtained in the first trial when the fungus was applied at 6 × 10⁷ conidia per ml. Final mortality of all species, except A. hybridus, reached 100% in inoculated plots 25 days earlier than in noninoculated control plots. Conidial suspensions were more effective in controlling the species in the second trial than were mycelial suspensions. Spread of the pathogen to noninoculated control plots was faster in the second year than in other years. High levels of plant mortality were achieved in plots of A. spinosus, A. lividus, and A. viridis. A. hybridus and the triazine-resistant A. hybridus were not effectively controlled in the second year due to the advanced stage of plant growth (8 to 10 true leaves) at the time of pathogen application. Results confirmed that P. amaranthicola is an effective biocontrol agent of some of the Amaranthus spp. tested.