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Synthetic data starch potato system Veenkoloniën

Synthetic generated with a simulation model for the starch potato production systems in the Veenkoloniën

opencc-by-4.0Dec 2020View details →

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The proximity interactome of the peach-potato aphid (Myzus persicae) cathepsin B in Arabidopsis thaliana

Introduction In agriculture, the peach-potato aphid Myzus persicae (Sulzer) has one of the broadest host ranges among insects and cause devastating crop losses worldwide (CABI, 2022). They are highly adaptable, displaying a wide range of plastic responses to environmental cues, including the ability to develop as either winged or wingless forms and to reproduce through either asexual or sexual means (Brisson, 2010; Ogawa and Miura, 2014; Grantham and Brisson, 2018). Remarkably, M. persicae differentially regulate the transcription of certain gene clusters to facilitate colonization of diverse plant species (Mathers et al., 2017; Chen et al., 2020). Among these gene clusters are members of the cysteine protease family, cathepsin B (CathB). Host responsive CathB genes are organized in tandemly repeated clusters in the M. persicae genome and belong to a recently expanded clade in phylogeny (Mathers et al., 2017). They are upregulated when aphids feed on Arabidopsis thaliana and Brassica rapa and knock down of their expression using RNA interference reduces aphid reproduction on A. thaliana (Chen et al., 2020). Intriguingly, peptides corresponding to CathB proteins are detected in M. persicae oral secretion (OS), indicating that at least some CathB proteins are directly delivered into plant cells during aphid feeding (Guo et al., 2020; Liu et al., 2024). Among M. persicae CathB proteins, CathB6 is most highly expressed in aphids on A. thaliana (Chen et al., 2020) and most abundant in M. persicae OS (Liu et al., 2024). To identify the potential plant targets of M. persicae CathB, we optimized the TurboID-based proximity labelling and MS (PL-MS) protocol (Fig. 1). As a first step, we generated stable transgenic A. thaliana lines producing GFP or CathB6 as C-terminal TurboID-3×FLAG fusions (GFP-TurboID or CathB6-TurboID). Seedlings of these plants were treated with biotin followed by affinity capture with streptavidin beads (Fig. 2A). Enrichment of biotinylated proteins was confirmed by western blotting (Fig. 2B), followed by nanoLC-MS/MS analyses. Principal component analysis (PCA) of the MS data showed that the three CathB6-TurboID samples were grouped together, separately from three GFP-TurboID samples (Fig. 2C). Furthermore, MA plot confirmed that the CathB6-TurboID and GFP-TurboID samples are distinct (Fig. 2D). From the complete dataset, 267 A. thaliana proteins exhibited statistically significant enrichment (p-value < 0.05) of more than 2-fold and were consistently identified in at least two replicates of the CathB6-TurboID samples compared to the GFP-TurboID controls (Fig. 2E, Table 1). This compares to 223 proteins in the GFP-TurboID samples versus CathB6-TurboID samples (Fig. 2E, Table 1). Additionally, we identified 20 unique peptides corresponding to CathB6 in the CathB6-TurboID samples and 19 unique peptides corresponding to GFP in the GFP-TurboID samples (Table 1). These data suggest that this PL-MS protocol worked dnd identified genuine interactors of CathB6. Together, this dataset identifies 267 potential plant interactors of aphid CathB6, which may contribute to CathB6 modulation of A. thaliana plant for colonization. Further mechanistic studies should be done to characterize if these potential interactors are involved and how the relevant pathways are affected after CathB delivery through aphid feeding.   Materials and Methods Plasmid construction For the construction of plasmids producing CathB6-TurboID-3×FLAG, the coding sequences corresponding to the catalytic domain (without signal peptide and prodomain regions) of CathB6 (Arg61-Asn338) and TurboID-3×FLAG were separately amplified. Then, the two fragments were connected using overlap PCR (Nelson and Fitch, 2011). After cloning of the sequence corresponding to the CathB6-TurboID-3×FLAG fragment into the pJET vector and sequencing, CathB6-TurboID-3×FLAG was amplified with primers containing attB extensions and cloned into the pDONOR207 vector, followed by the ligation to Gateway destination vector pB7WG2 containing a 35S promoter. Similar cloning methods were used for construction of GFP-TurboID-3×FLAG. Plant transformation The constructed plasmids were introduced into Agrobacterium tumefaciens strain GV3101, and the cultures were grown on plates at 28 °C for 24–48 hrs. Then, positive colonies were identified via PCR using plasmids extracted from overnight liquid cultures and gene-specific primers. Positive colonies were grown at 28 °C in liquid cultures and transformed into A. thaliana Col-0 plants using the floral dipping method (Bechtold, 1993). Transgenic seeds were harvested and selected on Murashige and Skoog (MS) medium supplemented with 20 μg/mL phosphinothricin (BASTA) and screened for ratio of 3:1 alive/dead segregation. After screening for two or three generations, transgenic plants were deemed to harbor single homozygous transgenes and were used for proximity labeling once germinated seeds achieved a 100% survival rate. Proximity labelling Seeds of A. thaliana plants stably expressing GFP-TurboID-3×FLAG or CathB6-TurboID-3×FLAG were sowed on ½ MS plates containing 1.0% sucrose and 0.3% phytagel and placed under long-day condition (16 h light/8 h dark) at 22 °C. After 10 days, 2.5 g seedlings were collected and submerged in 50 µM biotin solution for 4 hrs at RT. Afterwards, seedlings were rinsed with ice-cold MilliQ water for 5 times. After removing excess liquid with paper towel, seedings were ground with pestle, mortar and nitrogen to a fine powder. Protein extraction was performed in 5 mL of extraction buffer [150 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 10% Glycerol, 10 mM DTT, 0.4% Nonidet-40, 0.1% (w/v) Deoxycholic acid, 2% (w/v) PVPP, 1 tablet of cOmplete protease Inhibitor cocktail (Roche, Catalog number 10697498001)] and incubation on a rotor wheel at 4 °C for 30 min, followed by centrifugation of the tubes at 5000 g for 15 min to remove the cell debris. The upper soluble fraction was then run through the Zeba Spin Desalting Column (Thermo Fisher Scientific, Catalog number 89893) to remove excess biotin from the lysates. Fifty (50) µL of desalted lystate was used as input for western blot analysis, while the rest of the desalted lysate was incubated with High Capacity Streptavidin Agarose Resin (Thermo Fisher Scientific, Catalog number 20361) on a rotor wheel at 4 °C overnight. The next day, Streptavidin beads were sequentially washed once in 1 mL Buffer 1 (2% SDS in water), once in 1 mL Buffer 2 [150 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.1% (w/v) Deoxycholic acid (w/v), 1% Triton X-100], once in buffer 3 [10 mM Tris-HCl (pH 7.4), 250 mM LiCl, 1 mM EDTA, 0.1% (w/v) Deoxycholic acid, 1% (v/v) NP40], twice in Buffer 4 [50mM Tris-HCl (pH 7.5)], and six times in Buffer 5 (50mM ammonium bicarbonate, pH 8.0). Finally, the streptavidin beads were resuspended in 200 µL of 50 mM ammonium bicarbonate. For quality control of the TurboID immunoprecipitation, 10% (20 µL) of the suspension was taken out for Western blot analysis, and the remaining bead suspension was flash-frozen in liquid nitrogen and stored at -80 °C and submitted to nano LC-MS/MS analysis. For western blot analysis, 20 µL of suspended streptavidin beads in washing buffer 5 were added to 10 µL of 4× LDS Sample Loading Buffer, 10 mM DTT and 2 mM biotin, and boiled for 10 min. Samples were loaded onto 12% SDS-PAGE gels (Invitrogen) and transferred to 0.22 μm PVDF membranes using the Bio-Rad mini-PROTEAN Electrophoresis system. Membranes were hybridized with Streptavidin-HRP. NanoLC-MS/MS  Biotinylated proteins enriched with streptavidin beads were processed with trypsin via on bead digestion. The beads were washed in water and resuspended in of 1.5% sodium deoxycholate (SDC; Merck) in 0.2 M EPPS-buffer (Merck) to 50% bead slurry vol/vol, pH 8.5 and vortexed under heating. Cysteine residues were reduced with dithiothreitol, alkylated with iodoacetamide, and the proteins digested with trypsin in the SDC buffer according to standard procedures for 8 hrs. The beads were then pelleted by centrifugation and the supernatant was collected for SDC precipitation by adding trifluoroacetic acid (TFA) to a final concentration of 0.2%. The clear supernatant was subjected to C18 SPE using home-made stage tips with C18 Reprosil_pur 120, 5 µm (Dr. Maisch GmbH, Germany). Aliquots were analyzed by nano LC-MS/MS on an Orbitrap Eclipse™ Tribrid™ mass spectrometer equipped with a FAIMS Pro Duo interface coupled to an UltiMate® 3000 RSLC nano LC system (Thermo Fisher Scientific, Hemel Hempstead, UK). The samples were loaded onto a trap cartridge (PepMap™ Neo Trap Cartridge, C18, 5um, 0.3x5mm, Thermo) with 0.1% TFA at 15 µl min-1 for 3 min. The trap column was then switched in-line with the analytical column (Aurora Frontier TS, 60 cm nanoflow UHPLC column, ID 75 µm, reversed phase C18, 1.7 µm, 120 Å; IonOpticks, Fitzroy, Australia) for separation at 55°C using the following gradient of solvents: A (water, 0.1% formic acid) and B (80% acetonitrile, 0.1% formic acid) at a flow rate of 0.26 µl min-1 : 0-3 min 1% B (parallel to trapping); 3-10 min increase B (curve 4) to 8%; 10-102 min linear increase B to 48; followed by a ramp to 99% B and re-equilibration to 0% B. Total runtime was 140 min. Mass spectrometry data were acquired between 10 and 110 min with the FAIMS device set to three compensation voltages (-35V, -50V, -65V) at standard resolution for 1.0 s each with the following MS settings in positive ion mode: OT resolution 120K, profile mode, mass range m/z 300-1600, normalized AGC target 100%, max inject time 50 ms; MS2 in IT Turbo mode: quadrupole isolation window 1 Da, charge states 2-5, threshold 1e4, HCD CE = 30, AGC target standard, max. injection time dynamic, dynamic exclusion 1 count for 15 s with mass tolerance of ±10 ppm, one charge state per precursor only. The mass spectrometry raw data were processed and quantified in Proteome Discoverer 3.1 (PD3.1) (Thermo) using the search engine CHIMERYS (MSAID, Munich, Germany); all mentioned tools of the following workflow are nodes of the proprietary Proteome Discoverer (PD) software. The A. thaliana protein sequence database (TAIR10, 35,386 entries, from 14/12/2010), the two sequences of the used TurboID constructs, and the MaxQuant contaminants database (240812, 246 entries) were imported into PD adding a reversed sequence database for decoy searches. The database search was performed using the search engine CHIMERYS (MSAID, Munich, Germany). The processing workflow started with spectrum recalibration, Minora Feature Detection with min. trace length 5, S/N 2.5, PSM confidence high, and Top N Peak Filter with 20 peaks per 100 Da. For CHIMERYS, the inferys_3.0.0_fragmentation prediction model with FDR targets 0.01 (strict) and 0.05 (relaxed), a fragment tolerance of 0.3 Da, enzyme trypsin with 2 missed cleavages, variable modification oxidation (M), fixed modification carbamidomethyl (C) were used. The consensus workflow in the PD3.1 software was used to evaluate the peptide identifications and to measure the abundances of the peptides based on the LC-peak intensities. For chromatographic alignment and feature mapping, a retention time tolerance of 2 min, a mass tolerance of 1 ppm, and an S/N threshold of 5 were used. For quantification, three replicates per condition were measured. In PD3.1, the following parameters were used for ratio calculation: normalization on total peptide abundances, protein abundance-based ratio calculation using the Top3 most abundant peptides, missing values imputation by low abundance resampling, hypothesis testing by t-test (background based), adjusted p-value calculation by BH-method.  The results were exported into a Microsoft Excel table including data for protein abundances, ratios, p-values, number of peptides, protein coverage, the CHIMERYS identification score and other important values.   Data availability statement The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier with the dataset identifier PXD057789 and 10.6019/PXD057789.   Acknowledgements  This research was funded by UK Research and Innovation (UKRI) Biotechnology and Biological Sciences Research Council (BBSRC) grants to SAH (BB/V008544/1 and BB/R009481/1). Additional Support is provided by the BBSRC Institute Strategy Programmes (BBS/E/J/000PR9797 and BBS/E/JI/230001B) awarded to the JIC. The JIC is grant-aided by the John Innes Foundation.   Conflicts of Interest  The authors declare that no conflicts of interest exist.   Legends of figures and tables Figure 1. Principle of CathB6-TurboID based proximity labelling with MS (PL-MS). The TurboID biotin ligase (TurboID) is fused to C-terminus of CathB6. Exogenous addition of biotin (yellow stars) biotinylates proteins in the proximity of CathB6-TurboID fusion protein, whereas distal proteins are not biotinylated. The biotinylated proteins are captured by incubating total proteins extracts with streptavidin beads. Peptides derived from biotinylated proteins, most of which are in the proximity of CathB6-TurboID, are detected by nanoLC-MS. Fig. 2. Sample preparation and quantification for CathB6-TurboID interactome in A. thaliana. (A) Sample preparation working flow for TurboID-based proximity labeling. GFP-TurboID and CathB6-TurboID seedlings were treated with 50 µM biotin for 4 hrs at room temperature. (B) Visualization on western blots of biotinylated proteins detected after desalting step (input) and 12 wash steps of Streptavidin beads (Streptavidin IP) as per workflow shown in (A). (C) Principal component analysis (PCA) of three replicates of GFP-TurboID and CathB6-TurboID samples. (D) MA plot of three replicates of GFP-TurboID and CathB6-TurboID samples. (E) Venn diagrams showing the overlap of proteins identified in three biological replicates of GFP-TurboID (left) and CathB6-TurboID (right) upon a fold-change of CathB6-TurboID/GFP-TurboID > 2, n = 267.  Table 1. Full list of proteins detected from CathB6-TurboID PL-MS.     References Bechtold, N. (1993). In planta Agrobacterium-mediated gene transfer by infiltration of adult Arabidopsis thaliana plants. CR Acad. Sci. Paris, Life Sci. 316, 1194-1199. Brisson, J.A. (2010). Aphid wing dimorphisms: linking environmental and genetic control of trait variation. Philos Trans R Soc Lond B Biol Sci 365, 605-616. CABI, C.f.A.a.B.I. (2022). Myzus persicae (green peach aphid). CABI Compendium. Chen, Y., Singh, A., Kaithakottil, G.G., Mathers, T.C., Gravino, M., Mugford, S.T., van Oosterhout, C., Swarbreck, D., and Hogenhout, S.A. (2020). An aphid RNA transcript migrates systemically within plants and is a virulence factor. Proc Natl Acad Sci U S A 117, 12763-12771. Grantham, M.E., and Brisson, J.A. (2018). Extensive Differential Splicing Underlies Phenotypically Plastic Aphid Morphs. Mol Biol Evol 35, 1934-1946. Guo, H., Zhang, Y., Tong, J., Ge, P., Wang, Q., Zhao, Z., Zhu-Salzman, K., Hogenhout, S.A., Ge, F., and Sun, Y. (2020). An Aphid-Secreted Salivary Protease Activates Plant Defense in Phloem. Curr Biol 30, 4826-4836.e4827. Liu, Q., Goldberg, J.K., Mugford, S.T., Saalbach, G., Martins, C., Singh, A., Kaithakotti, G.G., Swarbreck, D., and Hogenhout, S.A. (2024). The salivary proteome of the green peach aphid/peach-potato aphid (Myzus persicae) (Sulzer, 1776) (Hemiptera, Aphididae) (Zenodo). Mathers, T.C., Chen, Y., Kaithakottil, G., Legeai, F., Mugford, S.T., Baa-Puyoulet, P., Bretaudeau, A., Clavijo, B., Colella, S., Collin, O., Dalmay, T., Derrien, T., Feng, H., Gabaldón, T., Jordan, A., Julca, I., Kettles, G.J., Kowitwanich, K., Lavenier, D., Lenzi, P., Lopez-Gomollon, S., Loska, D., Mapleson, D., Maumus, F., Moxon, S., Price, D.R., Sugio, A., van Munster, M., Uzest, M., Waite, D., Jander, G., Tagu, D., Wilson, A.C., van Oosterhout, C., Swarbreck, D., and Hogenhout, S.A.(2017). Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biol 18, 27. Nelson, M.D., and Fitch, D.H. (2011). Overlap extension PCR: an efficient method for transgene construction. Methods Mol Biol 772, 459-470. Ogawa, K., and Miura, T. (2014). Aphid polyphenisms: trans-generational developmental regulation through viviparity. Front Physiol 5, 1.

opencc-by-4.0Nov 2024View details →

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Data from 18 fungicide trials on potato late blight in UK and Ireland 2013-2017

The data set comprises records of disease incidence, crop growth stage and yield from untreated and treated plots. The data is provided as both a tab-separated text file and a binary R data file. The R files provides code to read and plot the data. The plot produced is also provided as a PNG file. The field trials were conducted by Corteva Agriscience, Germany.

opencc-by-4.0Mar 2022View details →

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Late blight resistance in potato conferred by Rpi-Smira2/R8

The data are related to Figure 7 of the publication Blatnik et al. (2022) Late blight resistance conferred by Rpi-Smira2/R8 in potato genotypes in vitro depends on the genetic background, published in Plants 11: 1319 (https://doi.org/10.3390/plants11101319) The data represent late blight (Phytophtora infestans) disease scores of progeny R8 genotypes and parental cultivars inoculated with four P. infestans isolates in vitro. The disease scores were evaluated daily for an eight day period post inoculation according to the late blight disease rating scale (see publication and info sheet of the data).

opencc-by-4.0May 2022View details →

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Dataset on consumers' perception of different types of sustainability levies, Swiss agriculture and farmers and willingness to choose suboptimal potatoes in different settings

This dataset includes survey data from 481 Swiss consumers. Data were collected in the German-speaking parts of Switzerland in February and March 2024. The survey includes three independent main parts. In a first part, we collected qualitative and quantitative data on participants’ perception of Swiss agriculture and farmers. Specifically, participants’ trust in crop and livestock production farmers and their perceived knowledge about production methods and their affect towards farmers was assessed. In a second part, we collected quantitative data on participants’ preference for different sustainability levies. For this, six different products were used (i.e., fresh/processed vegetables, dairy, and meat). For each of these six products, participants were shown four levy options from which they had to choose the one that they found most appealing. For vegetables, the options were: (A) reduction of risks related to plant protection products, (B) more support for local farmers, (C) support for environmental sustainability, and (D) sustainability projects in general. For the animal products, option (A) was an increase in animal welfare, whilst options (B), (C) and (D) were the same as for the vegetable products. In a third part, we collected qualitative and quantitative data on participants preferences for suboptimal or optimal potatoes. Here, a 2 × 2 experimental design (setting × information) was used. This means that participants were presented with either a supermarket or farm shop setting and with or without food waste information. Participants then chose between two potatoes: optimal potato A, suboptimal potato B, or neither. Both potatoes were equally expensive.

opencc-by-4.0Sep 2024View details →

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Publication & Supplementary data: Pro-health compounds and antioxidant activity of 65 potato cultivars

Metadata (climatic conditions, list of varieties, field plan, etc.) and data (carotenoid content, vitamin C content, radical scavenging activity DPPH and FRAP, yellow index) related to the paper of Tatarowska et al., "The content of total carotenoids, vitamin C and antioxidant properties of 65 potato cultivars characterised under the European project ECOBREED" published in Int. J. Mol. Sci. 24 (2023), 11716.

opencc-by-4.0Jun 2023View details →

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Really a nontraded commodity? A look at the international potato trade network (dataset and R code)

This archive contains code and data for a social network analysis of international potato trade that was published at https://perspectivesandforesight.wordpress.com/2012/11/08/really-a-nontraded-commodity-a-look-at-the-international-potato-trade-network/ on 08 November, 2012. It can serve as a reference for understanding the analysis, and as a basis for replication of the results as well as for carrying out more detailed analyses of international potato trade. The following information and data is included: - The R code used for the social network analysis of international potato trade. - Data files with bilateral matrices of global trade in fresh, frozen and seed potatoes. - Data files with supplementary data used for the analysis. - A copy of the original blog post that was written using the data and code provided herewith.

opencc-by-4.0Dec 2013View details →

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Figure 3 in On the successful acclimatization of the Colorado potato beetle Leptinotarsa decemlineata (Say, 1824) (Coleoptera: Chrysomelidae) in Primorsky kray

Figure 3. Modelling of the ecological niches of the Colorado potato beetle for the Far Eastern, European, and North American habitats by the method of metric two-dimensional

opencc-by-4.0Aug 2023View details →

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Investigating the Utility of Potato (Solanum tuberosum L.) Canopy Temperature and Leaf Greenness Responses to Water-Restriction for the Improvement of Irrigation Management Data

Traits that rapidly respond to stress in important agricultural crops have the potential to provide growers with actionable feedback. E.g., traits that respond to water-restriction could inform irrigation systems by identifying crop water status and requirements in real-time. This would be particularly useful for potato, which is extremely susceptible to drought. We conducted two pot experiments and one field experiment to evaluate the utility of two traits, canopy temperature and leaf greenness, for informing irrigation management in potatoes. We also evaluated the efficacy of Phenospex PlantEye F500 sensors for the remote sensing of leaf greenness. We found that canopy temperatures of the cvs. Maris Piper (Spring Pot Experiment, +0.8°C; Autumn Pot Experiment, +5.3°C) and Désirée (Autumn Pot Experiment, +2.5°C) increased with water-restriction and that the canopy temperatures of Maris Piper return to baseline within three days after the resumption of well-watered conditions. We also found that these responses varied between cultivars, with predictable outcomes based on reported and corroborated drought tolerance ratings. We found inconclusive evidence of leaf greenness increasing due to water-restriction (Spring Pot Experiment, +0.8°C; Autumn Pot Experiment, +5.3°C) and found no evidence that post-drought recovery periods return this trait to baseline. However, leaf greenness measurements from the Phenospex PlantEye F500 were moderately to strongly correlated with SPAD values, suggesting this tool might be useful in the screening of drought-tolerant cultivars in the future.

opencc-by-4.0Mar 2024View details →

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Fig. 1 in Protease inhibitors of fodder plants as a factor of immune response influencing the physiological state of the potato ladybird beetle Henosepilachna vigintioctomaculata (Coleoptera: Coccinellidae)

Fig. 1. Analysis of the population of the potato ladybird beetle with the species-specific PCR-markers of the gene COI mtDNA. А – species-specific marker for H. vigintioctopunctata, 400 b.p.; Б – species-specific marker for H. vigintioctomaculata, 406 b.p.; М – marker of the lengths of fragments 100 b.p. ladder; 1–3 – Primorsky krai: Chuguevsky district; 4–6 – Amurskaya oblast; 7–17 – Primorsky krai: Timiryazevsky.

opencc-by-4.0Jan 2024View details →

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Fig. 3 in Protease inhibitors of fodder plants as a factor of immune response influencing the physiological state of the potato ladybird beetle Henosepilachna vigintioctomaculata (Coleoptera: Coccinellidae)

Fig. 3. Sinergetic activity of the protainases of trypsin type (in an insect) and trypsin inhibitors (in a plant) in the course of feeding on different potato varieties.

opencc-by-4.0Jan 2024View details →

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Figure 3 in On the successful acclimatization of the Colorado potato beetle Leptinotarsa decemlineata (Say, 1824) (Coleoptera: Chrysomelidae) in Primorsky kray

Figure 3. Modelling of the ecological niches of the Colorado potato beetle for the Far Eastern, European, and North American habitats by the method of metric two-dimensional scaling using the Jaccard coefficient.

opencc-by-4.0Aug 2023View details →

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Figure 1 in On the successful acclimatization of the Colorado potato beetle Leptinotarsa decemlineata (Say, 1824) (Coleoptera: Chrysomelidae) in Primorsky kray

Figure 1. Dynamics of the population size of the Colorado potato beetle over the year of the research (population peaks are shown on average for Primorsky Kray).

opencc-by-4.0Aug 2023View details →

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Custom codes in the potato NLRome paper

All custom scripts used in this study are available at GitHub (<a href="https://github.com/HongboDoll/PotatoPanNLRome">https://github.com/HongboDoll/PotatoNLRome</a>)

opencc-by-4.0Nov 2024View details →

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Data for: The transmission ability in a population of elite tetraploid potatoes

Data set for the research article: Assessing the transmission potential of elite tetraploid potatoes. The dataset includes pedigree and phenotypic data of 5013 clones of an F1 population derived from an incomplete diallel cross of 18 parents of either established cultivars or elite breeding material from Danespo A/S across three market segments (starch, processing, and table). A total of 10 phenotypes are included, namely dry matter content, yield, senescence, skin finish, flesh color, length/width ratio, length, diameter, tubers/plant, and eye depth. In addition, GBS genotype data for a set of 93,170 biallelic SNPs filtered to MAF > 1 %, coverage > 5 and < 60, and missing rate < 70 %. Pedigree (A), genomic (G), and single-step combined (H) matrices are included.  A README file is included with descriptions of all provided data files.

opencc-by-4.0Oct 2024View details →

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Source data for gamete binning for an autotetraploid potato cultivar Otava

Here we provide the source data for analyzing a highly heterozygous autotetraploid potato cultivar 'Otava'.

opencc-by-4.0Dec 2021View details →

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Data from: Virus infection and host plant suitability affect feeding behaviors of cannabis aphid (Hemiptera: Aphididae), a newly described vector of potato virus Y

Aphids are the most prolific vectors of plant viruses resulting in significant yield losses to crops worldwide. Potato virus Y (PVY) is transmitted in a non-persistent manner by 65 species of aphids. With the increasing acreage of hemp (Cannabis sativa L.) (Rosales: Cannabaceae) in the U.S, we were interested to know if the cannabis aphid (Phorodon cannabis Passerini) (Hemiptera: Aphididae) is a potential vector of PVY. Here, we conduct transmission assays and utilize the electrical penetration graph (EPG) technique to determine whether cannabis aphids can transmit PVY to hemp (host) and potato (non-host) (Solanum tuberosum L.) (Solanales: Solanaceace). We show for the first time that the cannabis aphid is an efficient vector of PVY to hemp (96%) and potato (91%) using cohorts of aphids. In contrast, individual aphids transmitted the virus more efficiently to hemp (63%) compared to potato (19%). During the initial 15 minutes of EPG recordings, aphids demonstrated lower number and time spent performing intracellular punctures on potato compared to hemp, which may in part explain low virus transmission to potato using individual aphids. During the entire 8-hour recording, viruliferous aphids spent less time ingesting phloem compared to non-viruliferous aphids on hemp. This reduced host suitability could potentially cause aphids to disperse to more suitable hosts thereby increasing virus transmission. Overall, our study shows that cannabis aphid is an efficient vector of PVY, and that virus infection and host plant suitability affect feeding behaviors of the cannabis aphid in ways which may increase virus transmission.

opencc-zeroJan 2022View details →

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Fig. 2 in Current Distribution Of Golden Potato Cyst Nematode, Globodera Rostochiensis (Tylenchida, Heteroderidae), In Ukraine

Fig. 2. Occurrence of Golden potato cyst nematode, Globodera rostochiensis, on the territory of Ukraine: A — Volynska; B — Rivnenska; C — Zhytomyrska; D — Kyivska; E — Сhernihivska; F — Sumska; G — Lvivska; H — Ternopilska; I — Khmelnytska; J — Cherkaska; K — Poltavska; L — Kharkivska; M — Luhanska; N — Zakarpatska; O — Ivano-Frankivska; P — Chernivetska; Q — Vinnytska; R — Kirovogradska; S — Dnipropetrovska; T — Donetska; U — Odeska; V— Mylolaivska; W — Khersonska; X — Zaporizka; Y — AR Krym.

opencc-by-4.0Dec 2021View details →

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Fig. 1 in Current Distribution Of Golden Potato Cyst Nematode, Globodera Rostochiensis (Tylenchida, Heteroderidae), In Ukraine

Fig. 1. Study area of monitoring survey of G. rostochiensisin soils of private farm plots (own data, 2017–2018) 1. Chernihiv Region: а — Horodniansky District; b — Chernihivsky District; c — Mensky District; d — Koryukivsky District; e — Novhorod-Siversky District. 2. Kyiv Region: а — Borodiansky District.

opencc-by-4.0Dec 2021View details →

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Fig. 3 in Communities Of Ditylenchus Destructor Satellite Species Of Nematodes In Infected Potato Tubers: Species Composition Of Phytonematode Complex And The Structure Of Their Infracommunities

Fig. 3. The dynamics of the ratio of the total number of various trophoecological group nematodes during the disease of potato tubers caused by D. destructor.

opencc-by-4.0Nov 2019View details →

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Allen Brain Atlas

Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.

allen-brain-atlas

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Last verified 2026-04-30Open record

Annotated Behaviour and Observability Dataset (ABODe)

ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.

abode-home-cage

behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.

Last verified 2026-04-30Open record

DANDI Archive for NWB datasets

DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.

dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

International Brain Laboratory public data

The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

OpenNeuro

OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.

openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record