Using next-generation sequencing to detect mutations endowing resistance to pesticides: application to acetolactate-synthase (ALS)-based resistance in barnyard grass, a polyploid grass weed

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.

Deep haplotype analyses of target-site resistance locus ACCase in blackgrass enabled by pool-based amplicon sequencing

Rapid adaptation of weeds to herbicide applications in agriculture through resistance development is a widespread phenomenon. In particular, the grass Alopecurus myosuroides is an extremely problematic weed in cereal crops with the potential to manifest resistance in only a few generations. Target-site resistances (TSRs), with their strong phenotypic response, play an important role in this rapid adaptive response. Recently, using PacBio's long-read amplicon sequencing technology in hundreds of individuals, we were able to decipher the genomic context in which TSR mutations occur. However, sequencing individual amplicons are costly and time-consuming, thus impractical to implement for other resistance loci or applications. Alternatively, pool-based approaches overcome these limitations and provide reliable allele frequencies, although at the expense of not preserving haplotype information. In this proof-of-concept study, we sequenced with PacBio High Fidelity (HiFi) reads long-range amplicons (13.2 kb), encompassing the entire ACCase gene in pools of over 100 individuals, and resolved them into haplotypes using the clustering algorithm PacBio amplicon analysis (pbaa), a new application for pools in plants and other organisms. From these amplicon pools, we were able to recover most haplotypes from previously sequenced individuals of the same population. In addition, we analysed new pools from a Germany-wide collection of A. myosuroides populations and found that TSR mutations originating from soft sweeps of independent origin were common. Forward-in-time simulations indicate that TSR haplotypes will persist for decades even at relatively low frequencies and without selection, highlighting the importance of accurate measurement of TSR haplotype prevalence for weed management.

Target-Site Mutations and Expression of ALS Gene Copies Vary According to Echinochloa Species

The sustainability of rice cropping systems is jeopardized by the large number and variety of populations of polyploid Echinochloa spp. resistant to ALS inhibitors. Better knowledge of the Echinochloa species present in Italian rice fields and the study of ALS genes involved in target-site resistance could significantly contribute to a better understanding of resistance evolution and management. Using a CAPS-rbcL molecular marker, two species, E. crus-galli (L.) P. Beauv. and E. oryzicola (Vasinger) Vasing., were identified as the most common species in rice in Italy. Mutations involved in ALS inhibitor resistance in the different species were identified and associated with the ALS homoeologs. The relative expression of the ALS gene copies was evaluated. Molecular characterization led to the identification of three ALS genes in E. crus-galli and two in E. oryzicola. The two species also carried different point mutations conferring resistance: Ala122Asn in E. crus-galli and Trp574Leu in E. oryzicola. Mutations were carried in the same gene copy (ALS1), which was significantly more expressed than the other copies (ALS2 and ALS3) in both species. These results explain the high resistance level of these populations and why mutations in the other ALS copies are not involved in herbicide resistance.

RNA-Seq transcriptome analysis to identify candidate genes involved in non-target site-based mesosulfuron-methyl resistance in Beckmannia syzigachne

American sloughgrass (Beckmannia syzigachne Steud.) has become a dominant weed in fields with rice-wheat rotation. Moreover, herbicide resistance has rendered weed control difficult. We identified a biotype showing resistance to ALS inhibitor mesosulfuron-methyl with a resistant index 3.3, but without any ALS mutation. This study aims to identify and confirm the factors associated with non-target site resistance of this biotype to mesosulfuron-methyl using RNA-Seq. 118,111 unigenes were assembled, and 50.9% of these were annotated across seven databases. Eleven contigs related to metabolic resistance were identified based on differential expression via RNA-Seq which include a novel resistance-related transcription factor (MYC3) and two disease resistance proteins were also identified (At1g58602 and At1g15890). Fold changes in expression of these genes in comparison M-R vs. M-S ranged from 3.9 to 11.6, as confirmed by qPCR. The expression of a contig annotated as cytochrome P450 (CYP86B1) in resistant individuals was over 3 times higher than that in sensitive individuals at 0-72 h after mesosulfuron-methyl treatment. A similar trend was noted for three other genes annotated as glutathione S-transferase (GST), namely GST-T3, GST-U6, and GST-U14; the expression of GST-U6 in resistant individuals was up to 142.3 times higher than that in sensitive individuals at 24 h after mesosulfuron-methyl treatment. In addition, GST activity in resistant individuals was 2.1 to 5.3 times higher than that in sensitive individuals. The GR₅₀ of resistant biotype decreased from 24.4 to 11.3 g a.i. ha^-1 after P450 inhibitor malathion treatment. This study identified a cytochrome P450 gene CYP86B1 and three GST genes GST-T3, GST-U6, and GST-U14 that have higher expression in mesosulfuron-methyl resistant B. syzigachne, suggesting that both P450- and GST-based activities could be involved in resistance.

Harnessing the power of next-generation sequencing technologies to the purpose of high-throughput pesticide resistance diagnosis

BACKGROUND

Next Generation Sequencing (NGS) technologies offer tremendous possibilities for high-throughput pesticide resistance diagnosis via massive genotyping-by-sequencing. Herein, we used Illumina sequencing combined with a simple, non-commercial bioinformatics pipe-line to seek mutations involved in herbicide resistance in two weeds.

RESULTS

DNA was extracted from 96 pools of 50 plants for each species. Three amplicons encompassing 15 ALS (acetolactate-synthase) codons crucial for herbicide resistance were amplified from each DNA extract. Above 18 and 20 million quality 250-nucleotide sequence reads were obtained for groundsel (Senecio vulgaris, tetraploid) and ragweed (Ambrosia artemisiifolia, diploid), respectively. Herbicide resistance-endowing mutations were identified in 45 groundsel and in eight ragweed field populations. The mutations detected and their frequencies assessed by NGS were checked by individual plant genotyping or Sanger sequencing. NGS results were fully confirmed, except in three instances out of 12 where mutations present at a frequency of 1% were detected below the threshold set for reliable mutation detection.

CONCLUSION

Analyzing 9600 plants requested 192 DNA extractions followed by 1728 PCRs and two Illumina runs. Equivalent results obtained by individual analysis would have necessitated 9600 individual DNA extractions followed by 216 000 genotyping PCRs, or by 121 500 PCRs and 40 500 Sanger sequence runs. This clearly demonstrates the interest and power of NGS-based detection of pesticide resistance from pools of individuals for diagnosing resistance in massive numbers of individuals. © 2019 Society of Chemical Industry.

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

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.

Genetic basis, evolutionary origin and spread of resistance to herbicides inhibiting acetolactate synthase in common groundsel (Senecio vulgaris)

BACKGROUND

Following control failure by herbicides inhibiting acetolactate synthase (ALS) in French wheat fields and vineyards, we aimed to confirm resistance evolution and investigate the evolutionary origin and spread of resistance in the tetraploid species Senecio vulgaris (common groundsel), a widespread, highly mobile weed.

RESULTS

Sequencing of two ALS homeologues in S. vulgaris enabled the first identification and characterisation of ALS-based resistance in this species. Cross-resistance patterns associated with Leu-197 and Ser-197 ALS1 were established using eight herbicides. Sequencing and genotyping showed that ALS-based resistance evolved by multiple, independent appearances of mutant ALS1 and ALS2 alleles followed by spread. Spread of a mutant ALS1 allele issued from one particular appearance event was observed over 60 km. Independent resistance appearance events and easy seed dispersion are the most likely reasons for populations of S. vulgaris containing different mutant ALS alleles. Accumulation of different alleles probably due to sexual reproduction was observed in the same plant.

CONCLUSION

Mutant ALS alleles and possibly other mechanisms cause resistance to ALS inhibitors in S. vulgaris. Management strategies should aim at limiting S. vulgaris establishment and seed set. Considering the mobility of this species, control coordination at a regional level is clearly necessary if resistance spread is to be contained.