Adaptive and maladaptive expression plasticity underlying herbicide resistance in an agricultural weed.
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ABSTRACT:
SUBMITTER: Josephs EB
PROVIDER: S-EPMC8327940 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The repeated evolution of herbicide resistance has been cited as an example of genetic parallelism, wherein separate species or genetic lineages utilize the same genetic solution in response to selection. However, most studies that investigate the genetic basis of herbicide resistance examine the potential for changes in the protein targeted by the herbicide rather than considering genome-wide changes. We used a population genomics screen and targeted exome re-sequencing to uncover the potential genetic basis of glyphosate resistance in the common morning glory, Ipomoea purpurea, and to determine if genetic parallelism underlies the repeated evolution of resistance across replicate resistant populations. We found no evidence for changes in 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), glyphosate's target protein, that were associated with resistance, and instead identified five genomic regions that showed evidence of selection. Within these regions, genes involved in herbicide detoxification-cytochrome P450s, ABC transporters, and glycosyltransferases-are enriched and exhibit signs of selective sweeps. One region under selection shows parallel changes across all assayed resistant populations whereas other regions exhibit signs of divergence. Thus, while it appears that the physiological mechanism of resistance in this species is likely the same among resistant populations, we find patterns of both similar and divergent selection across separate resistant populations at particular loci.
| S-EPMC7018220 | biostudies-literature
Project description:Human-mediated selection can lead to rapid evolution in very short time scales, and the evolution of herbicide resistance in agricultural weeds is an excellent example of this phenomenon. The common morning glory, Ipomoea purpurea, is resistant to the herbicide glyphosate, but genetic investigations of this trait have been hampered by the lack of genomic resources for this species. Here, we present the annotated transcriptome of the common morning glory, Ipomoea purpurea, along with an examination of whole genome expression profiling to assess potential gene expression differences between three artificially selected herbicide resistant lines and three susceptible lines. The assembled Ipomoea transcriptome reported in this work contains 65,459 assembled transcripts, ~28,000 of which were functionally annotated by assignment to Gene Ontology categories. Our RNA-seq survey using this reference transcriptome identified 19 differentially expressed genes associated with resistance-one of which, a cytochrome P450, belongs to a large plant family of genes involved in xenobiotic detoxification. The differentially expressed genes also broadly implicated receptor-like kinases, which were down-regulated in the resistant lines, and other growth and defense genes, which were up-regulated in resistant lines. Interestingly, the target of glyphosate-EPSP synthase-was not overexpressed in the resistant Ipomoea lines as in other glyphosate resistant weeds. Overall, this work identifies potential candidate resistance loci for future investigations and dramatically increases genomic resources for this species. The assembled transcriptome presented herein will also provide a valuable resource to the Ipomoea community, as well as to those interested in utilizing the close relationship between the Convolvulaceae and the Solanaceae for phylogenetic and comparative genomics examinations.
| S-EPMC4199709 | biostudies-literature
Project description:BACKGROUND AND AIMS: Selective pressures exerted by agriculture on populations of arable weeds foster the evolution of adaptive traits. Germination and emergence dynamics and herbicide resistance are key adaptive traits. Herbicide resistance alleles can have pleiotropic effects on a weed's life cycle. This study investigated the pleiotropic effects of three acetyl-coenzyme A carboxylase (ACCase) alleles endowing herbicide resistance on the seed-to-plant part of the life cycle of the grass weed Alopecurus myosuroides. METHODS: In each of two series of experiments, A. myosuroides populations with homogenized genetic backgrounds and segregating for Leu1781, Asn2041 or Gly2078 ACCase mutations which arose independently were used to compare germination dynamics, survival in the soil and seedling pre-emergence growth among seeds containing wild-type, heterozygous and homozygous mutant ACCase embryos. KEY RESULTS: Asn2041 ACCase caused no significant effects. Gly2078 ACCase major effects were a co-dominant acceleration in seed germination (1·25- and 1·10-fold decrease in the time to reach 50 % germination (T50) for homozygous and heterozygous mutant embryos, respectively). Segregation distortion against homozygous mutant embryos or a co-dominant increase in fatal germination was observed in one series of experiments. Leu1781 ACCase major effects were a co-dominant delay in seed germination (1·41- and 1·22-fold increase in T50 for homozygous and heterozygous mutant embryos, respectively) associated with a substantial co-dominant decrease in fatal germination. CONCLUSIONS: Under current agricultural systems, plants carrying Leu1781 or Gly2078 ACCase have a fitness advantage conferred by herbicide resistance that is enhanced or counterbalanced, respectively, by direct pleiotropic effects on the plant phenology. Pleiotropic effects associated with mutations endowing herbicide resistance undoubtedly play a significant role in the evolutionary dynamics of herbicide resistance in weed populations. Mutant ACCase alleles should also prove useful to investigate the role played by seed storage lipids in the control of seed dormancy and germination.
| S-EPMC3605953 | biostudies-literature
Project description:Phenotypic plasticity enables a single genotype to produce multiple phenotypes in response to environmental variation. Plasticity may play a critical role in the colonization of novel environments, but its role in adaptive evolution is controversial. Here we suggest that rapid parallel regulatory adaptation of Anolis lizards to urban heat islands is due primarily to selection for reduced and/or reversed heat-induced plasticity that is maladaptive in urban thermal conditions. We identify evidence for polygenic selection across genes of the skeletal muscle transcriptome associated with heat tolerance. Forest lizards raised in common garden conditions exhibit heat-induced changes in expression of these genes that largely correlate with decreased heat tolerance, consistent with maladaptive regulatory response to high-temperature environments. In contrast, urban lizards display reduced gene expression plasticity after heat challenge in common garden and a significant increase in gene expression change that is congruent with greater heat tolerance, a putatively adaptive state in warmer urban environments. Genes displaying maladaptive heat-induced plasticity repeatedly show greater genetic divergence between urban and forest habitats than those displaying adaptive plasticity. These results highlight the role of selection against maladaptive regulatory plasticity during rapid adaptive modification of complex systems in the wild.
| S-EPMC8548502 | biostudies-literature
Project description:Adaptive phenotypic plasticity may improve the response of individuals when faced with new environmental conditions. Typically, empirical evidence for plasticity is based on phenotypic reaction norms obtained in reciprocal transplant experiments. In such experiments, individuals from their native environment are transplanted into a different environment, and a number of trait values, potentially implicated in individuals' response to the new environment, are measured. However, the interpretations of reaction norms may differ depending on the nature of the assessed traits, which may not be known beforehand. For example, for traits that contribute to local adaptation, adaptive plasticity implies nonzero slopes of reaction norms. By contrast, for traits that are correlated to fitness, high tolerance to different environments (possibly due to adaptive plasticity in traits that contribute to adaptation) may, instead, result in flat reaction norms. Here we investigate reaction norms for adaptive versus fitness-correlated traits and how they may affect the conclusions regarding the contribution of plasticity. To this end, we first simulate range expansion along an environmental gradient where plasticity evolves to different values locally and then perform reciprocal transplant experiments in silico. We show that reaction norms alone cannot inform us whether the assessed trait exhibits locally adaptive, maladaptive, neutral, or no plasticity, without any additional knowledge of the traits assessed and species' biology. We use the insights from the model to analyse and interpret empirical data from reciprocal transplant experiments involving the marine isopod Idotea balthica sampled from two geographical locations with different salinities, concluding that the low-salinity population likely has reduced adaptive plasticity relative to the high-salinity population. Overall, we conclude that, when interpreting results from reciprocal transplant experiments, it is necessary to consider whether traits assessed are locally adaptive with respect to the environmental variable accounted for in the experiments or correlated to fitness.
| S-EPMC9923493 | biostudies-literature
Project description:Since 1996, genetically modified herbicide-resistant (HR) crops, particularly glyphosate-resistant (GR) crops, have transformed the tactics that corn, soybean, and cotton growers use to manage weeds. The use of GR crops continues to grow, but weeds are adapting to the common practice of using only glyphosate to control weeds. Growers using only a single mode of action to manage weeds need to change to a more diverse array of herbicidal, mechanical, and cultural practices to maintain the effectiveness of glyphosate. Unfortunately, the introduction of GR crops and the high initial efficacy of glyphosate often lead to a decline in the use of other herbicide options and less investment by industry to discover new herbicide active ingredients. With some exceptions, most growers can still manage their weed problems with currently available selective and HR crop-enabled herbicides. However, current crop management systems are in jeopardy given the pace at which weed populations are evolving glyphosate resistance. New HR crop technologies will expand the utility of currently available herbicides and enable new interim solutions for growers to manage HR weeds, but will not replace the long-term need to diversify weed management tactics and discover herbicides with new modes of action. This paper reviews the strengths and weaknesses of anticipated weed management options and the best management practices that growers need to implement in HR crops to maximize the long-term benefits of current technologies and reduce weed shifts to difficult-to-control and HR weeds.
| S-EPMC3105486 | biostudies-literature
Project description:Herbicide resistance in grass weeds is now one of the greatest threats to sustainable cereal production in Northern Europe. Multiple-herbicide resistance (MHR), a poorly understood multigenic and quantitative trait, is particularly problematic as it provides tolerance to most classes of chemistries currently used for post-emergence weed control. Using a combination of transcriptomics and proteomics, the evolution of MHR in populations of the weed blackgrass (Alopecurus myosuroides) has been investigated. While over 4500 genes showed perturbation in their expression in MHR versus herbicide sensitive (HS) plants, only a small group of proteins showed >2-fold changes in abundance, with a mere eight proteins consistently associated with this class of resistance. Of the eight, orthologues of three of these proteins are also known to be associated with multiple drug resistance (MDR) in humans, suggesting a cross-phyla conservation in evolved tolerance to chemical agents. Proteomics revealed that MHR could be classified into three sub-types based on the association with resistance to herbicides with differing modes of action (MoA), being either global, specific to diverse chemistries acting on one MoA, or herbicide specific. Furthermore, the proteome of MHR plants were distinct from that of HS plants exposed to a range of biotic (insect feeding, plant-microbe interaction) and abiotic (N-limitation, osmotic, heat, herbicide safening) challenges commonly encountered in the field. It was concluded that MHR in blackgrass is a uniquely evolving trait(s), associated with changes in the proteome that are distinct from responses to conventional plant stresses, but sharing common features with MDR in humans.
| S-EPMC5969246 | biostudies-literature
Project description:Gene amplification has been observed in many bacteria and eukaryotes as a response to various selective pressures, such as antibiotics, cytotoxic drugs, pesticides, herbicides, and other stressful environmental conditions. An increase in gene copy number is often found as extrachromosomal elements that usually contain autonomously replicating extrachromosomal circular DNA molecules (eccDNAs). Amaranthus palmeri, a crop weed, can develop herbicide resistance to glyphosate [N-(phosphonomethyl) glycine] by amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene, the molecular target of glyphosate. However, biological questions regarding the source of the amplified EPSPS, the nature of the amplified DNA structures, and mechanisms responsible for maintaining this gene amplification in cells and their inheritance remain unknown. Here, we report that amplified EPSPS copies in glyphosate-resistant (GR) A. palmeri are present in the form of eccDNAs with various conformations. The eccDNAs are transmitted during cell division in mitosis and meiosis to the soma and germ cells and the progeny by an as yet unknown mechanism of tethering to mitotic and meiotic chromosomes. We propose that eccDNAs are one of the components of McClintock's postulated innate systems [McClintock B (1978) Stadler Genetics Symposium] that can rapidly produce soma variation, amplify EPSPS genes in the sporophyte that are transmitted to germ cells, and modulate rapid glyphosate resistance through genome plasticity and adaptive evolution.
| S-EPMC5879691 | biostudies-literature
Project description:Acetyl-CoA carboxylase (ACCase) alleles carrying one point mutation that confers resistance to herbicides have been identified in arable grass weed populations where resistance has evolved under the selective pressure of herbicides. In an effort to determine whether herbicide resistance evolves from newly arisen mutations or from standing genetic variation in weed populations, we used herbarium specimens of the grass weed Alopecurus myosuroides to seek mutant ACCase alleles carrying an isoleucine-to-leucine substitution at codon 1781 that endows herbicide resistance. These specimens had been collected between 1788 and 1975, i.e., prior to the commercial release of herbicides inhibiting ACCase. Among the 734 specimens investigated, 685 yielded DNA suitable for PCR. Genotyping the ACCase locus using the derived Cleaved Amplified Polymorphic Sequence (dCAPS) technique identified one heterozygous mutant specimen that had been collected in 1888. Occurrence of a mutant codon encoding a leucine residue at codon 1781 at the heterozygous state was confirmed in this specimen by sequencing, clearly demonstrating that resistance to herbicides can pre-date herbicides in weeds. We conclude that point mutations endowing resistance to herbicides without having associated deleterious pleiotropic effects can be present in weed populations as part of their standing genetic variation, in frequencies higher than the mutation frequency, thereby facilitating their subsequent selection by herbicide applications.
| S-EPMC3797703 | biostudies-literature
Project description:Deep-water (DW) management in rice fields is a promising technique for efficient control of paddy weeds with reduced herbicide use. Maintaining a water depth of 10-20 cm for several weeks can largely suppress the weed growth, though it also inhibits rice growth because the DW management is usually initiated immediately after transplanting. Improving the DW resistance of rice during the initial growth stage is essential to avoid suppressing growth. In this study, we demonstrate a large genetic variation in the above-ground biomass (AGB) after the end of DW management among 165 temperate japonica varieties developed in Japan. Because the AGB closely correlated with plant length (PL) and tiller number (TN) at the early growth stage, we analyzed genomic regions associated with PL and TN by conducting a genome-wide association study. For PL, a major peak was detected on chromosome 3 (qPL3), which includes a gene encoding gibberellin biosynthesis, OsGA20ox1. The rice varieties with increased PL had a higher expression level of OsGA20ox1 as reported previously. For TN, a major peak was detected on chromosome 4 (qTN4), which includes NAL1 gene associated with leaf morphological development and panicle number. Although there was less difference in the expression level of NAL1 between genotypes, our findings suggest that an amino acid substitution in the exon region is responsible for the phenotypic changes. We also found that the rice varieties having alternative alleles of qPL3 and qTN4 showed significantly higher AGB than the varieties with the reference alleles. Our results suggest that OsGA20ox1 and NAL1 are promising genes for improving DW resistance in rice.
| S-EPMC10676340 | biostudies-literature