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

Abstract

This work demonstrated the feasibility of NGS-based detection of pesticide resistance, and the advantages of NGS compared with other molecular biology techniques for analysing large numbers of individuals. NGS-based resistance diagnosis has the potential to play a substantial role in monitoring resistance, maintaining pesticide efficacy and optimising pesticide applications.

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

“…Molecular assays allowing rapid processing of a large number of samples and accurate identification of resistant plants will certainly be helpful in implementing resistance management strategies against S. vulgaris . Next‐generation sequencing‐based assays have proven to be of great interest for this purpose . Such assays can easily be developed for S. vulgaris , especially because of the absolute sequence conservation of ALS1 and ALS2 around this codon in S. vulgaris .…”

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

“…The threshold was based on the expected frequency of one allele having a mutation in the pooled sample. As the average pool size was 24 samples, the expected frequency was 1 of 48 alleles …”

“…There are three dominant NGS technologies: 454 (pyrosequencing; Rochs, Branfors, CT, USA), Illumina's (highly parallel sequencing by synthesis; Illumina, San Diego, CA, USA), and SOLiD (sequencing by ligation; Applied Biosystems, Foster City, CA, USA) . The 454‐technology has been used as an efficient method in detecting mutations of the ALS gene in ALS‐inhibitor‐resistant weeds . However, the Illumina MiSeq platform provides greater read depth, fewer sequencing errors, and lower per‐base cost than 454 technology .…”

Utilizing next-generation sequencing to study homeologous polymorphisms and herbicide-resistance-endowing mutations inPoa annuaacetolactate synthase genes

“…However, the application of NGS in weed species is lagging behind that in model plants and crop species . To date, no complete genome has been assembled from any weed species, and only a small number of publications have reported the use of NGS for assembly and analysis of transcriptome or chloroplast genome, for marker development and for addressing herbicide/pesticide resistance problems in weed species …”

“…5 To date, no complete genome has been assembled from any weed species, and only a small number of publications have reported the use of NGS for assembly and analysis of transcriptome or chloroplast genome, 6 -9 for marker development 7,8,10,11 and for addressing herbicide/pesticide resistance problems in weed species. 12 -14 Poa annua is one of the most widespread grass species worldwide. It is adapted to diverse environments, including extreme areas such as remote subarctic meadows, 15 the Antarctic Peninsula 16 and Mount Kilimanjaro in Africa close to the equator.…”