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39 results for “oilseed rape”
Annotated patches of whole oilseed rape (Brassica napus) plant images created using the MapReader pipeline
<p><strong>Background and Dataset Creation:</strong></p> <p>Patches derived from whole images of oilseed rape (<em>Brassica napus</em>) plants from the <a href="https://research.aber.ac.uk/en/datasets/collection-of-side-view-and-top-view-rgb-images-of-brassica-napus">'Collection of side view and top view RGB images of Brassica napus from a large scale, high throughput experiment'</a> dataset and their associated annotations, which were used to train, validate and test patch classification models as described in the following paper:</p> <p>Corcoran, E., Hosseini, K., Siles, L., Kurup, S., and Ahnert, S. 2024. 'Automated dynamic phenotyping of whole oilseed rape (Brassica napus) plants from images collected under controlled conditions', Frontiers in Plant Science (under review). </p> <p>Patches were created and annotated using the <a href="https://github.com/Living-with-machines/MapReader">MapReader</a> pipeline. Please see: </p> <ul> <li>Kasra Hosseini, Daniel C. S. Wilson, Kaspar Beelen, and Katherine McDonough. 2022. MapReader: a computer vision pipeline for the semantic exploration of maps at scale. In Proceedings of the 6th ACM SIGSPATIAL International Workshop on Geospatial Humanities (GeoHumanities '22). Association for Computing Machinery, New York, NY, USA, 8–19. <a href="https://doi.org/10.1145/3557919.3565812" rel="nofollow">https://doi.org/10.1145/3557919.3565812</a></li> <li>Kasra Hosseini, Rosie Wood, Andy Smith, Katie McDonough, Daniel C.S. Wilson, Christina Last, Kalle Westerling, and Evangeline Mae Corcoran. “Living-with-machines/mapreader: End of Lwm”. Zenodo, July 27, 2023. <a href="https://doi.org/10.5281/zenodo.8189653" rel="nofollow">https://doi.org/10.5281/zenodo.8189653</a>.</li> </ul> <p><strong>File structure:</strong></p> <p><em><strong>Annotations</strong></em></p> <p>The <strong>'annotations_six_label_sv_5.zip'</strong> folder contains annotations for the entire patch dataset in .csv format, these files have two columns <strong>'image_id'</strong>, <strong>'label'</strong> in which:</p> <ul> <li><strong>'image_id'</strong> = the path to each image patch</li> <li><strong>'label'</strong> = the label assigned to each patch by the annotator indicated which part of the plant the patch primarily contained, or if it was part of the background. Labels: <strong>'0'</strong> = non-plant background, <strong>'1'</strong> = open flower, <strong>'2'</strong> = flower bud, <strong>'3'</strong> = leaf, <strong>'4'</strong> = greed pod containing seed, <strong>'5'</strong> = branch. </li> </ul> <p><em><strong>Patches</strong></em></p> <p>The 'b_napus_patch_data.zip' folder contains all patches in csv format. Each file is named in a consistent format e.g. "patch-1580-330-1590-340-#2018-07-06_00_VIS_sv_000-0-0-0.png#.PNG" where '1580-330-1590-340' are the x and y coordinates of the patch boundary and '#2018-07-06_00_VIS_sv_000-0-0-0.png#' indicates the image in the <a href="https://research.aber.ac.uk/en/datasets/collection-of-side-view-and-top-view-rgb-images-of-brassica-napus">'Collection of side view and top view RGB images of Brassica napus from a large scale, high throughput experiment'</a> from which the patch was derived. </p>
Data for: Proximity to oilseed rape fields affects plant pollination and pollinator-mediated selection on a co-flowering plant on the Tibetan Plateau
<p><span>The ecological effects of mass-flowering crops on pollinator abundance and species richness of neighboring habitats are well established, yet the potential evolutionary consequences remain unclear. We studied effects of proximity to a mass-flowering crop on the pollination of local co-flowering plants, and on patterns of natural selection on a pollination-generalized plant on the Tibetan Plateau. We recorded pollinator visitation rates and community composition at different distances (near vs. far) to oilseed rape (Brassica napus) fields in two habitat types, and quantified pollinator-mediated selection on attractive traits of Trollius ranunculoides. The proximity to oilseed rape increased pollinator visitation in neighboring alpine meadows and changed pollinator composition in neighboring shrub meadows. Trollius ranunculoides in the alpine meadow near oilseed rape received three times more pollinator visits (mainly bees), and consequently had a 16.5% increase in seed set, but also received slightly more heterospecific pollen per stigma. In contrast, pollinator visitation to T. ranunculoides in the shrub meadow near oilseed rape was three times lower (mainly flies), leading to 10.7% lower seed despite no effect on pollen deposition. The proximity to the oilseed rape field intensified pollinator-mediated selection on flower size and weakened selection on flower height of T. ranunculoides in the alpine meadow but did not affect phenotypic selection on either trait in the shrub meadow. Our study highlights context-dependent variation in plant-pollinator interactions close to mass-flowering oilseed rape, suggesting potential effects on the evolution of flower traits of native plants through altered pollinator-mediated selection. However, context dependence may make these effects difficult to predict.</span></p>
Exploring multitrophic interactions in oilseed rape fields reveals the prevailing role of Carabidae
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Data from: Flower fields and pesticide use interactively shape pollen beetle infestation and parasitism in oilseed rape fields.
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Data from: The relation between oilseed rape and pollination of later flowering plants varies across plant species and landscape contexts
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Data for: Proximity to oilseed rape fields affects plant pollination and pollinator-mediated selection on a co-flowering plant on the Tibetan Plateau
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Data from: Migration patterns and changes in population biology associated with the worldwide spread of the oilseed rape pathogen Leptosphaeria maculans
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Data from: Genetic diversity of oilseed rape fields and feral populations in the context of coexistence with GM crops
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Data from: Agri-environmental schemes promote ground-dwelling predators in adjacent oilseed rape fields: diversity, species traits and distance-decay functions
1. Rising demands for agricultural products and high environmental costs of intensive agriculture reinforce the need for ecological replacements in agricultural management. In Europe, agri-environmental schemes (AES) are implemented to enhance species richness and provision of ecosystem services, but the effectiveness of different AES types and the spatial extent of possible beneficial effects are little understood. In this study we assessed the effects of different AES types on diversity, species traits and distance-decay functions of ground- dwelling predators in adjacent crop fields. 2. On 31 study sites with winter oilseed rape (OSR) adjacent to four types of AES differing in management intensity and habitat age we recorded ground-dwelling predators (carabid beetles, staphylinid beetles and spiders) during OSR growth from April to July. Effects of the AES on species richness, activity densities and different traits of these taxa were examined with transects of pitfall traps running along a continuous distance gradient from the AES across the habitat border into the OSR fields. 3. Ground-dwelling predator communities benefitted similarly from the different AES types. In adjacent OSR, activity densities, carabid species richness and the proportion of predatory carabid beetles declined from the field edge while mean body size increased. Adjacent AES increased the proportion of predatory species and simultaneously decreased the proportion of granivorous or frugivorous species in adjacent OSR fields. 4. Synthesis and applications. Our results indicate a beneficial effect of adjacent agri-environmental schemes (AES) on ground-dwelling predators in oilseed rape (OSR), mostly irrespective of AES type and therefore management intensity and habitat age. The short-ranged distance decay effects on natural enemies in OSR underpin that a strategic spatial placement of AES in agricultural landscapes is required to maximise biological pest control. This could help replace anthropogenic input in modern agriculture and secure adequate yields.
Direct access to millions of mutations by Whole Genome Sequencing of an oilseed rape mutant population
<p>Induced mutations are an essential source of genetic variation in plant breeding. EMS mutagenesis has been frequently applied, and mutants have been detected by phenotypic or genotypic screening of large populations. In this study, a rapeseed M<sub>2</sub> population was derived from M<sub>1</sub> parent cultivar “Express” treated with EMS. Whole genomes were sequenced from fourfold (4x) pools of 1,988 M<sub>2</sub> plants representing 497 M<sub>2</sub> families. Detected mutations were not evenly distributed and displayed distinct patterns across the 19 chromosomes with lower mutation rates towards the ends. Mutation frequencies ranged from 32/Mb to 48/Mb. On average, 284,442 single nucleotide polymorphisms per M<sub>2</sub> DNA pool were found resulting from EMS mutagenesis. 55% were C→T and G→A transitions, characteristic for EMS induced (‘canonical’) mutations, whereas the remaining SNPs were ‘non-canonical’ transitions (15%) or transversions (30%). Additionally, we detected 88,725 high confidence insertions and deletions (InDels) per pool. On average, each M<sub>2</sub> plant carried 39,120 canonical mutations, corresponding to a frequency of one mutation per 23.6 kb. Roughly 82% of such mutations were located either 5 kb upstream or downstream (~56%) of gene coding regions or within intergenic regions (26%). The remaining 18% were located within regions coding for genes. All mutations detected by whole-genome sequencing could be verified by comparison with known mutations. Furthermore, all sequences are accessible via the online tool “EMS Brassica” (<a href="http://www.emsbrassica.plantbreeding.uni-kiel.de/">http://www.emsbrassica.plantbreeding.uni-kiel.de/</a>), which enables direct identification of mutations in any target sequence. The sequence resource described here will further add value for functional gene studies in rapeseed breeding.</p>
Data from: Agri-environmental schemes promote ground-dwelling predators in adjacent oilseed rape fields: diversity, species traits and distance-decay functions
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Small RNAs in different tissues and phloem of oilseed rape under nutrient stress conditions
GEO Series GSE20263. Pinus taeda; Glycine max; Medicago truncatula; Selaginella moellendorffii; Populus trichocarpa; Brassica napus; Brassica oleracea; Physcomitrium patens; Arabidopsis thaliana; Brassica rapa; Oryza sativa; Saccharum officinarum; Triticum aestivum; Sorghum bicolor; Zea mays; Vitis vinifera. 10 samples. Type: Non-coding RNA profiling by array.
RNA-seq experiments of systemic colonization of oilseed rape by Leptosphaeria maculans
GEO Series GSE81756. Brassica napus; Plenodomus lingam. 18 samples. Type: Expression profiling by high throughput sequencing.
Comparative transcriptomic analyses of Spring OilSeed Rape (SOSR)accessions in response to warm temperature.
GEO Series GSE173272. Brassica napus. 12 samples. Type: Expression profiling by high throughput sequencing.
Nitrogen starvation and cultivar-specific leaf senescence in winter oilseed rape (Brassica napus)
GEO Series GSE60108. Brassica napus. 24 samples. Type: Expression profiling by array.
Leptosphaeria maculans gene expression during in vitro growth and primary oilseed rape leaf infection
GEO Series GSE27152. Plenodomus lingam; Brassica napus. 9 samples. Type: Expression profiling by array.
Comparative transcriptomic analyses of Winter OilSeed Rape (WOSR) accessions during the germination process
GEO Series GSE137230. Brassica napus. 15 samples. Type: Expression profiling by high throughput sequencing.
Identification and characterization of miRNAs in oilseed rape (Brassica napus) responsive to the pathogenic fungus Verticillium longisporum infection using Brassica AA (B. rapa) and CC (B. oleracea) a
GEO Series GSE58322. Brassica napus. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Leptosphaeria maculans gene expression at the beginning of primary oilseed rape leaf infection
GEO Series GSE55456. Brassica napus; Plenodomus lingam. 3 samples. Type: Expression profiling by array.
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