Biology subjects

MacGregor, D. R.

Publications and source records attributed to MacGregor, D. R..

6 recordsLinked to original sources

bioRxiv2025

Insights from controlled, comparative experiments highlight the limitations of using BSMV and FoMV for virus-enabled reverse genetics in rice

1.Virus-enabled reverse genetics (VERG) is a powerful tool for transient gene expression modulation in plants, particularly where stable transformation is challenging. However, the efficacy of VERG varies across species. In this study, we tested two commonly used viral vectors, barley stripe mosaic virus (BSMV) and foxtail mosaic virus (FoMV), for their ability to induce virus-induced gene silencing (VIGS) and virus-mediated overexpression (VOX) in rice (Oryza sativa L.). While both vectors successfully altered gene expression in wheat (Triticum aestivum), they failed to do so in six rice cultivars from different subspecies, despite rigorous optimization of inoculation methods and environmental conditions. The BSMV vector carrying antisense phytoene desaturase (PDS) sequences did not induce the expected photobleaching phenotype, and FoMV-driven GFP expression was absent in rice. These findings contrast with previous reports of successful VERG in other monocots and suggest that intrinsic resistance mechanisms exist in rice which may inhibit or reduce viral vector efficacy. Our results highlight the species-specific limitations of VERG and underscore the need for alternative viral systems or novel vector designs for functional genomics research in rice. By sharing our unsuccessful attempts, we aim to prevent redundant efforts and encourage further exploration of VERG in Oryza species.

plant biology↗

bioRxiv2024

Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis.

Alopecurus aequalis is a winter annual or short-lived perennial bunchgrass which has in recent years emerged as the dominant agricultural weed of barley and wheat in certain regions of China and Japan, causing significant yield losses. Its robust tillering capacity and high fecundity, combined with the development of both target and non-target-site resistance to herbicides means it is a formidable challenge to food security. Here we report on a chromosome-scale assembly of A. aequalis with a genome size of 2.83 Gb. The genome contained 33,758 high-confidence protein-coding genes with functional annotation. Comparative genomics revealed that the genome structure of A. aequalis is more similar to Hordeum vulgare rather than the more closely related Alopecurus myosuroides and has undergone an expansion of cytochrome P450 genes, a gene family involved in non-target-site herbicide resistance.

plant biology↗

bioRxiv2024

Group 15 Pre-emergent Herbicides Differentially Effect Plant Growth, Cuticular Wax Composition, and Fatty Acid Metabolism in Herbicide-Resistant and Herbicide-naïve Blackgrass

Despite their long history of effective use in agroecosystems, the precise molecular mechanisms of many pre-emergent herbicides are not fully understood. This study investigates the effects of three Group 15 pre-emergent herbicides (Flufenacet, S-ethyl dipropylthiocarbamate (EPTC), and tri-allate) on two well-characterized blackgrass (Alopecurus myosuroides) biotypes. Blackgrass is the predominant weed threatening winter wheat production in North-West Europe and the effective use of pre-emergent herbicides is important for preventing otherwise difficult-to-control blackgrass from establishing in agricultural fields. Using a sterile, agar-based system, we quantified the effects of multiple doses of flufenacet, EPTC, or tri-allate on plant physiology, including germination and early seedling growth, as well as the effects of a single dose on key biochemical pathways, specifically cuticular wax composition and fatty acid metabolism in biotypes exhibiting either non-target site herbicide resistance or complete sensitivity to all tested herbicides. Our data demonstrate that the three Group 15 pre-emergent herbicides alter cuticular wax composition and fatty acid profiles differently and that the resistant and herbicide-naive biotypes show distinct responses to each herbicide. The GC-FID and GC-MS data from the different Group 15 pre-emergent herbicides are consistent with the observed differences in physiology and identify potential differences in how and where these herbicides act in these biotypes. Our findings provide novel molecular insights into the mechanisms of action of and tolerance to flufenacet, EPTC, or tri-allate in blackgrass.

plant biology↗

bioRxiv2023

The International Weed Genomics Consortium: Community Resources for Weed Genomics Research

The International Weed Genomics Consortium is a collaborative group of researchers focused on developing genomic resources for the study of weedy plants. Weeds are attractive systems for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Our goal is to use genomic information to develop sustainable and effective weed control methods and to provide insights about biotic and abiotic stress tolerance to assist crop breeding. Here, we outline resources under development by the consortium and highlight areas of research that will be impacted by these enabling resources.

genomics↗

bioRxiv2021

The blackgrass genome reveals patterns of divergent evolution of non-target site resistance to herbicides.

Globally, weedy plants result in more crop yield loss than plant pathogens and insect pests combined. Much of the success of weeds rests with their ability to rapidly adapt in the face of human-mediated environmental management and change. The evolution of resistance to herbicides is an emblematic example of this rapid adaptation. Here, we focus on Alopecurus myosuroides (blackgrass), the most impactful agricultural weed in Europe. To gain insights into the evolutionary history and genomic mechanisms underlying adaptation in blackgrass, we assembled and annotated its large, complex genome. We show that non-target site herbicide resistance is oligogenic and likely evolves from standing genetic variation. We present evidence for divergent selection of resistance at the level of the genome in wild, evolved populations, though at the transcriptional level, resistance mechanisms are underpinned by similar patterns of up-regulation of stress- and defence-responsive gene families. These gene families are expanded in the blackgrass genome, suggesting that the large, duplicated, and dynamic genome plays a role in enabling rapid adaptation in blackgrass. These observations have wide significance for understanding rapid plant adaptation in novel stressful environments.

genomics↗

bioRxiv2020

Virus-mediated transient expression techniques enable genetic modification of Alopecurus myosuroides

Even though considerable progress has been made in weed ecology, weed molecular biology has been hindered by an inability to genetically manipulate weeds. Genetic manipulation is essential to demonstrate a causative relationship between genotype and phenotype. Herein we demonstrate that virus-mediated transient expression techniques developed for other monocots can be used in black-grass (Alopecurus myosuroides) for loss- and gain-of-function studies. We not only use virus induced gene silencing (VIGS) to create the black-grass exhibiting reduced PHYTOENE DESATURASE expression and virus-mediated overexpression (VOX) to drive GREEN FLUORESCENT PROTEIN, we demonstrate these techniques are applicable to testing hypotheses related to herbicide resistance in black-grass. We use VIGS to demonstrate that AmGSTF1 is necessary for the resistant biotype Peldon to survive fenoxaprop application and show the heterologous expression of the bialaphos resistance gene with VOX is sufficient to confer resistance to an otherwise lethal dose of glufosinate. Black-grass is the most problematic weed for winter-cereal farmers in the UK and Western Europe as it has rapidly evolved adaptions that allow it to effectively avoid current integrated weed management practices. Black-grass also reduces yields and therefore directly threatens food security and productivity. Novel disruptive technologies which mitigate resistance evolution and enable better control over this pernicious weed are therefore required. These virus-mediated protocols offer a step change in our ability to alter genes of interest under controlled laboratory conditions and therefore to gain a molecular-level understanding of how black-grass can survive in the agri-environment. One Sentence SummaryVirus-mediated transient expression techniques create loss- and gain-of-function mutations in black-grass and show causation between specific genotypes and measurable changes in herbicide resistance.

genetics↗