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72 results for “Clover”
Data from: Annual flower strips support pollinators and potentially enhance red clover seed yield
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Pollination and plant reproductive success of two ploidy levels in red clover (Trifolium pratense L.)
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Data from: Contrasting the effects of natural selection, genetic drift and gene flow on urban evolution in white clover (Trifolium repens)
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Data from: Searching for the bull's-eye: agents and targets of selection vary among geographically disparate cyanogenesis clines in white clover (Trifolium repens L.)
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Premating isolation in neopolyploid red clover (Trifolium pratense)
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Different pollination approaches to compare the seed set of diploid and tetraploid red clover (Trifolium pratense L.)
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Data from: Evolution of drought resistance strategies following the introduction of white clover (Trifolium repens L.)
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Data from: Aridity shapes cyanogenesis cline evolution in white clover (Trifolium repens L.)
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Data from: Landscape composition has limited impact on local genetic structure in mountain clover, Trifolium montanum L.
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Data from: Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium)
Background: Some clover species, particularly Trifolium subterraneum, have previously been reported to have highly unusual plastomes, relative to closely related legumes, enlarged with many duplications, gene losses and the presence of DNA unique to Trifolium, which may represent horizontal transfer. In order to pinpoint the evolutionary origin of this phenomenon within the genus Trifolium, we sequenced and assembled the plastomes of eight additional Trifolium species widely sampled from across the genus. Results: The Trifolium plastomes fell into two groups: those of Trifolium boissieri, T. strictum and T. glanduliferum (representing subgenus Chronosemium and subg. Trifolium section Paramesus) were tractable, assembled readily and were not unusual in the general context of Fabeae plastomes. The other Trifolium species ("core Trifolium") proved refractory to assembly mainly because of numerous short duplications. These species form a single clade, which we call the "refractory clade" (comprising subg, Trifolium sections Lupinaster, Trifolium, Trichocephalum, Vesicastrum and Trifoliastrum). The characteristics of the refractory clade are the presence of numerous short duplications and 7-15% longer genomes than the tractable species. Molecular dating estimates that the origin of the most recent common ancestor (MRCA) of the refractory clade is approximately 13.1 million years ago (MYA). This is considerably younger than the estimated MRCA ages of Trifolium (c. 18.6 MYA) andTrifolium subg. Trifolium (16.1 MYA). Conclusions: We conclude that the unusual repetitive plastome type previously characterized in Trifolium subterraneum had a single origin within Trifolium and is characteristic of most (but not all) species of subgenus Trifolium. It appears that an ancestral plastome within Trifolium underwent an evolutionary change resulting in plastomes that either actively promoted, were permissive to, or were unable to control, duplications within the genome. The precise mechanism of this important change in the mode and tempo of plastome evolution deserves further investigation.
Data from: Recurrent gene deletions and the evolution of adaptive cyanogenesis polymorphisms in white clover (Trifolium repens L.)
Understanding the molecular evolution of genes that underlie intraspecific polymorphisms can provide insights into the process of adaptive evolution. For adaptive polymorphisms characterized by gene presence/absence (P/A) variation, underlying loci commonly show signatures of long-term balancing selection, with gene-presence and gene-absence alleles maintained as two divergent lineages. We examined the molecular evolution of two unlinked P/A polymorphisms that underlie a well-documented adaptive polymorphism for cyanogenesis (hydrogen cyanide release with tissue damage) in white clover. Both cyanogenic and acyanogenic plants occur in this species, and the ecological forces that maintain this chemical defense polymorphism have been studied for several decades. Using a sample of 65 plants, we investigated the molecular evolution of sequences flanking the two underlying cyanogenesis genes: Ac/ac (controlling the presence/absence of cyanogenic glucosides), and Li/li (controlling the presence/absence of their hydrolyzing enzyme, linamarase). A combination of genome-walking, PCR assays, DNA sequence analysis, and Southern blotting was used to test whether these adaptive P/A polymorphisms show evidence of long-term balancing selection, or whether gene-absence alleles have evolved repeatedly through independent deletion events. For both loci, we detect no signatures of balancing selection in closest flanking genomic sequences. Instead, we find evidence for variation in the size of the deletions characterizing gene-absence alleles. These observations strongly suggest that both of these polymorphisms have been evolving through recurrent gene deletions over time. We discuss the genetic mechanisms that could account for this surprising pattern and the implications of these findings for mechanisms of rapid adaptive evolution in white clover.
Irish Grass Clover Dataset (VistaMilk)
<p>Irish grass clover dataset<br>Overview</p> <p><br>The Irish Grass Clover Dataset, collected in Ireland by a group of researchers working at the VistaMilk Science Foundation Ireland Research Centre , comprises high-resolution images of herbage biomass. The dataset includes ground-truth annotations for herbage mass (kg DM/ha) and post-cutting herbage height (cm), capturing the composition percentages of grass, weed, and clover. This document provides details about the dataset, including collection methods, image specifications, and associated ground-truth data.</p> <p><br>Dataset description</p> <p><br>The dataset contains multiple subsets of data collected using a tripod mounted camera, a handheld phone or a drone. The dataset can be divided into two main subsets: the Camera & Phone Images subset and the Drone Images subset. </p> <p><br>Camera & Phone Images:</p> <p><br>This dataset was gathered in 2020 in Ireland using both a high-resolution Canon camera (Canon EOS 90D Camera - Canon Europe) and a smartphone camera (iPhone 6). All the images were collected at Moorepark Farm managed by Teagasc, aiming to capture the biomass composition comprising grass, weeds and clover. Each image corresponded to a 0.5×0.5 m quadrat with 5-6 images taken for each of the 26 plots.<br>Ground truth (GT) is provided for a subset of these images while other images are collected without GT. The herbage within quadrats for which GT was collected was harvested at 2-4 cm above ground level using Gardena hand shears (Accu 60, Gardena International GmbH, Ulm, Germany) immediately after image capture. Fresh weight was recorded and the harvested herbage was separated, oven-dried for 16 hours and weighed to give dry matter yield.</p> <p><br>For each of the GT images the following labels are provided: total dry herbage mass (kg DM/ha), dry grass biomass percentage (%), dry clover biomass percentage (%), dry weed biomass percentage (%), fresh grass biomass percentage (%), fresh clover biomass percentage (%), fresh weed biomass percentage (%), and sward height post-cutting (cm). Additional views were taken using the smartphone for validation and generalisation purposes. All labelled phone images were collected at the exact same quadrats/locations where some of the camera images were taken, therefore they share the same GT values. A larger number of unlabeled camera & phone images were also collected at random locations across the same plots where the labelled images were collected.</p> <p><br>The contents of this subset can be summarised as:<br>* 525 GT camera images divided into 418 train set labelled images and 107 validation set labelled images.<br>* 124 GT phone images divided into 17 train set labelled images and 107 validation set labelled images.<br>* 1072 unlabelled camera images <br>* 1112 unlabelled phone images </p> <p> </p> <p><br>Drone Images</p> <p><br>An extension of the Camera & Phone Images subset was created in late Autumn of 2021 where drone images were collected in the same 23 herbage paddocks originally studied with camera & phone images. At each paddock between 7 to 36 drone images at an altitude between 6 and 12 metres were captured. The drone used is the DJI Mavic 2 Pro 1 with its default camera, taking pictures at a resolution of 5472 × 3648.<br>A total of 331 drone images with their associated altitude were obtained. Because of the huge areas covered by drone images, the ground-truth we collect is limited to the dry herbage mass at the paddock level and we omit the grass height and biomass percentage information. Two ground-truth estimation methods were utilised for the drone images: the first is a visual estimation performed on site at the time of the image collection by two human experts, the second is following the protocol of Egan et al. [1], where two 1.2 × 8 metres strips in the paddocks are cut at 4 cm above ground level (typical cow grazing height) using an Etesia lawn mower (Etesia UK. Ltd., Warwick, UK). A 100 grams sample is collected from the cut material and dried at 95°C for 16 hours to obtain the dry herbage mass.</p> <p><br>Structure</p> <p><br>The file structure for this repository is as follows:</p> <p><br>irish_dataset_all/<br> |_README.md<br> |<br> |_camera<br> | |_train.csv // training images (filenames and GT annotations)<br> | |_train_red.csv // a smaller training subset of 52 images names and annotations<br> | |_val.csv // validation images names and annotations<br> | |_images/ // The training and test camera images<br> |_phone<br> | |_phone_gt_train.csv // training images (filenames and GT annotations)<br> | |_phone_gt_train.csv // validation images (filenames and annotations)<br> | |_images/ // training and test phone images<br> | <br> |_camera_unlab // unlabeled Camera images<br> |<br> |_phone_unlab // unlabeled Phone images<br> |<br> |_drone <br> | |_images // Drone images, organized by paddock<br> | |_labels.csv // image filenames and associated paddock level herbage mass ground truth (including visually estimated)<br> | |_paddock_gt.csv // paddock level herbage mass ground truth (including visually estimated)</p> <p>License:</p> <p>This dataset is provided under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License (CC BY-NC-SA 4.0). <br>This means you are free to:<br>Share: Copy and redistribute the material in any medium or format.<br>Adapt: Remix, transform, and build upon the material.</p> <p>However, these permissions are subject to the following terms:<br>Attribution: You must give appropriate credit, provide a link to the license, and indicate if changes were made.<br>Non-Commercial: You may not use the material for commercial purposes.<br>ShareAlike: If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original.<br>By using this dataset, you agree to abide by these terms. For more details about the license, visit https://creativecommons.org/share-your-work/cclicenses/.</p> <p>Acknowledgements and fair use:</p> <p>Please cite us if our work and data helps your research !</p> <p><br>@inproceedings{albert2021semi,<br> title={Semi-supervised dry herbage mass estimation using automatic data and synthetic images},<br> author={Albert, Paul and Saadeldin, Mohamed and Narayanan, Badri and Mac Namee, Brian and Hennessy, Deirdre and O'Connor, Aisling and O'Connor, Noel and McGuinness, Kevin},<br> booktitle={Proceedings of the IEEE/CVF International Conference on Computer Vision},<br> pages={1284--1293},<br> year={2021}<br>}</p> <p><br>@inproceedings{albert2022unsupervised,<br> title={Unsupervised domain adaptation and super resolution on drone images for autonomous dry herbage biomass estimation},<br> author={Albert, Paul and Saadeldin, Mohamed and Narayanan, Badri and Mac Namee, Brian and Hennessy, Deirdre and O'Connor, Noel E and McGuinness, Kevin},<br> booktitle={Proceedings of the IEEE/CVF conference on computer vision and pattern recognition},<br> pages={1636--1646},<br> year={2022}<br>}</p> <p><br>@article{albert2022utilizing,<br> title={Utilizing unsupervised learning to improve sward content prediction and herbage mass estimation},<br> author={Albert, Paul and Saadeldin, Mohamed and Narayanan, Badri and Mac Namee, Brian and Hennessy, Deirdre and O'Connor, Aisling H and O'Connor, Noel E and McGuinness, Kevin},<br> journal={arXiv preprint arXiv:2204.09343},<br> year={2022}<br>}</p> <p><br>References<br>[1] Egan, Michael, Norann Galvin, and Deirdre Hennessy. "Incorporating white clover (Trifolium repens L.) into perennial ryegrass (Lolium perenne L.) swards receiving varying levels of nitrogen fertilizer: Effects on milk and herbage production." Journal of Dairy Science 101, no. 4 (2018): 3412-3427<br>[a]Get license added here.</p>
Figure 5 from: Scoppola A, Lattanzi E, Bernardo L (2016) Distribution and taxonomy of the Italian clovers belonging to Trifolium sect. Vesicastrum subsect. Mystillus (Fabaceae). Italian Botanist 2: 7-27. https://doi.org/10.3897/italianbotanist.2.10361
Figure 5 - Trifolium vesiculosum collected in Viterbo (bar = 1 mm). Flowers (4 July 2016), pod and seeds (2 August 2016).
Figure 4 from: Scoppola A, Lattanzi E, Bernardo L (2016) Distribution and taxonomy of the Italian clovers belonging to Trifolium sect. Vesicastrum subsect. Mystillus (Fabaceae). Italian Botanist 2: 7-27. https://doi.org/10.3897/italianbotanist.2.10361
Figure 4 - Trifolium mutabile collected in Viterbo (bar = 1 mm). Flowers (15 May 2015), seeds (15 July 2016).
Figure 2 from: Scoppola A, Lattanzi E, Bernardo L (2016) Distribution and taxonomy of the Italian clovers belonging to Trifolium sect. Vesicastrum subsect. Mystillus (Fabaceae). Italian Botanist 2: 7-27. https://doi.org/10.3897/italianbotanist.2.10361
Figure 2 - Comparison between mature calyces of Trifolium subsect. Mystillus species in Italy (bar = 1 mm). Left: Trifolium vesiculosum (A) and Trifolium spumosum (A'), middle Trifolium multistriatum transitional (B) and typical (B') forms, right Trifolium mutabile s.str. (C) and Trifolium mutabile var. gussoneanum (C').
Figure 1 from: Scoppola A, Lattanzi E, Bernardo L (2016) Distribution and taxonomy of the Italian clovers belonging to Trifolium sect. Vesicastrum subsect. Mystillus (Fabaceae). Italian Botanist 2: 7-27. https://doi.org/10.3897/italianbotanist.2.10361
Figure 1 - Flowering head of Trifolium multistriatum from Seminara (Reggio Calabria) (Photo by L. Bernardo, 1 June 2016).
Figure 3 from: Scoppola A, Lattanzi E, Bernardo L (2016) Distribution and taxonomy of the Italian clovers belonging to Trifolium sect. Vesicastrum subsect. Mystillus (Fabaceae). Italian Botanist 2: 7-27. https://doi.org/10.3897/italianbotanist.2.10361
Figure 3 - Trifolium multistriatum, transitional forms (bar = 1 mm). Fresh flowers (24 June 2016) and seeds (5 August 2016) from plants collected in Rionero in Vulture (Potenza); detailed calyces from a specimen collected in the Ofanto valley (Aquilonia, Avellino) (CLU).
Data from: Rapid evolution of an adaptive cyanogenesis cline in introduced North American white clover (Trifolium repens L.)
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Data from: Network size‐dependent impact on vegetative growth and sexual reproduction in clonal patches of white clover Trifolium repens
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Data from: Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium)
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