RNA-Seq transcriptome analysis of Amaranthus palmeri with differential tolerance to glufosinate herbicide

Abstract

Amaranthus palmeri (Amaranthaceae) is a noxious weed in several agroecosystems and in some cases seriously threatens the sustainability of crop production in North America. Glyphosate-resistant Amaranthus species are widespread, prompting the use of alternatives to glyphosate such as glufosinate, in conjunction with glufosinate-resistant crop cultivars, to help control glyphosate-resistant weeds. An experiment was conducted to analyze the transcriptome of A. palmeri plants that survived exposure to 0.55 kg ha-1 glufosinate. Since there was no record of glufosinate use at the collection site, survival of plants within the population are likely due to genetic expression that pre-dates selection; in the formal parlance of weed science this is described as natural tolerance. Leaf tissues from glufosinate-treated and non-treated seedlings were harvested 24 h after treatment (HAT) for RNA-Seq analysis. Global gene expression was measured using Illumina DNA sequence reads from non-treated and treated surviving (presumably tolerant, T) and susceptible (S) plants. The same plants were used to determine the mechanisms conferring differential tolerance to glufosinate. The S plants accumulated twice as much ammonia as did the T plants, 24 HAT. The relative copy number of the glufosinate target gene GS2 did not differ between T and S plants, with 1 to 3 GS2 copies in both biotypes. A reference cDNA transcriptome consisting of 72,780 contigs was assembled, with 65,282 sequences putatively annotated. Sequences of GS2 from the transcriptome assembly did not have polymorphisms unique to the tolerant plants. Five hundred sixty-seven genes were differentially expressed between treated T and S plants. Of the upregulated genes in treated T plants, 210 were more highly induced than were the upregulated genes in the treated S plants. Glufosinate-tolerant plants had greater induction of ABC transporter, glutathione S-transferase (GST), NAC transcription factor, nitronate monooxygenase (NMO), chitin elicitor receptor kinase (CERK1), heat shock protein 83, ethylene transcription factor, heat stress transcription factor, NADH-ubiquinone oxidoreductase, ABA 8’-hydroxylase, and cytochrome P450 genes (CYP72A, CYP94A1). Seven candidate genes were selected for validation using quantitative real time-PCR. While GST was upregulated in treated tolerant plants in at least one population, CYP72A219 was consistently highly expressed in all treated tolerant biotypes. These genes are candidates for contributing tolerance to glufosinate. Taken together, these results show that differential induction of stress-protection genes in a population can enable some individuals to survive herbicide application. Elevated expression of detoxification-related genes can get fixed in a population with sustained selection pressure, leading to evolution of resistance. Alternatively, sustained selection pressure could select for mutation(s) in the GS2 gene with the same consequence.

Effect of Phosphinothricin on Transgenic Downy Birch (Betula pubescens Ehrh.) Containing bar or GS1 Genes

“…After treatment by 200 g/ha or 400 g/ha of glufosinate-ammonium, cotton plants accumulated similar levels of ammonium, but only plants treated by 400 g/ha died [40]. Leaf disks of six PPP-sensitive Amaranthus palmeri genotypes accumulated on average two times more ammonium than six resistant genotypes, but the maximum for tolerant and the minimum for sensitive species were quite similar [45]. An insignificant increase in ammonium in subsequently dead birch saplings containing the GS gene suggests that it is not ammonium that causes their death.…”

“…Other attempts to use additional copies of natural GS genes to protect against PPT did not produce a clear positive result: only limited resistance to a low dose of herbicide has been shown for hybrid poplar [8] and rice [9,39]. Differences in resistance between different Amaranthus palmeri genotypes were also not associated with copy number or GS gene expression [45]. It is possible that the use of mutant GS genes will be more effective, but there are very few such studies, so very few glufosinate-resistant weeds are known.…”

The genetic architecture and genomic context of glyphosate resistance inAmaranthus tuberculatus

“…Ferredoxin NADPH reductase belongs to two synthetic enzymes (dicamba monooxygenase and glyphosate acetyltransferase) that are used to produce genetically modified herbicide resistant plants (Bruggeman et al, 2014;Gaines et al, 2020;Green & Owen, 2011); ERF0105 is differentially expressed in glufosinate treated A. thaliana (Salas-Perez et al, 2018); uridine kinase-like protein 3 mediates responses to glyphosate in A. thaliana (Faus et al, 2015;Luo et al, 2016); and glutamate receptors may be important, because glutamate uptake is altered by glyphosate (Gomes et al, 2014;Serra et al, 2013). In our set of genes, these may be those most likely to directly influence resistance to glyphosate herbicides, although it is statistically impossible to verify the strength of evidence for each of them.…”

Recurrent Selection by Herbicide Sublethal Dose and Drought Stress Results in Rapid Reduction of Herbicide Sensitivity in Junglerice

“…Scientific advances in NTSR research have helped in the identification and understanding of resistance mechanisms in herbicide metabolism and in the network of detoxification processes [22,23,65,75,[100][101][102][103][104]. Plants contain large numbers of UDP-glucose-dependent glycosyltransferases (UGTs), responsible for conjugating metabolites with acceptor molecules in phase II of xenobiotic metabolism [105,106].…”

“…Either type of mechanism can confer resistance to multiple herbicides; both types of mechanisms can occur in the same population or in the same plant, adding another layer of complexity [18]. Recent NTSR studies sought to elucidate the genetic mechanisms that confer and select resistance through detoxification of xenobiotics, with multi-omics approaches, in species such as Amaranthus palmeri, Conyza bonariensis, E. phyllopogon, E. crus-galli, and E. colona [19][20][21][22][23][24][25].…”