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12 research data, page 1 of 2

Single nucleotide polymorphism datasets from 52 highly diverse accessions of the model allopolyploid plant Brassica napus.

Schmutzer, Thomas (2015)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
Variant calling has been performed with three different prediction methods using the tools FaSD, Freebayes and samtools. This allowed us to use the variant caller count (VCC) as an additional confidence value for the prediction of variant positions (VP). The VCC indicates how many variant calling methods predict the particular VP. All displayed VPs succeed in at least one of the genotypes the following criteria: bi-allelic, SNP quality score >= 100, homozygous, read depth >= 4 and...

Animated movie of the high-resolution CT images of the developing Brassica napus seed

Verboeven, Pieter (2012)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
Whole rapeseeds were scanned using a high resolution X-ray micro-CT system. The X-ray shadow projections of the 3-D object were digitized as 2048 x 2048 pixel images and were processed to obtain reconstructed cross-section images using a mathematical algorithm based on the filtered back-projection procedure implemented in the NRecon 1.6.2.0 software. This resulted in a 3-D stack of 1500 virtual sections, each consisting of 1500 × 1500 isotropic voxels of (1.7 µm3) with a linear X-...

A Preliminary Review of Allium subg. Melanocrommyum in Central Asia

Fritsch, Reinhard M (2016)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
The review (288 pages A4) contains a taxonomic treatment of subg. Melanocrommyum (82 species and subspecies with about 40 synonyms, but no new taxa) affiliated to 17 sections and 21 subsections. Included is also subg. Porphyroprason (1 species, 2 synonyms). The publication starts with a Foreword, a General Introduction into the biological features of subg. Melanocrommyum, and an illustrated key (in color) for determination simultaneously in English and Russian on opposite pages. I...

15k SNP chip data for spring and winter wheat

Quddoos H Muqaddasi (2017)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
In total, 207 wheat genotypes (111 spring and 96 winter type) were analysed using a 15k Infinium SNP array, which is an optimized and reduced version of the 90k iSELECT SNP-chip described by Wang et al. (2014) Plant Biotechnol J 12:787-796. The development of the 15k SNP-chip and genotyping was performed by TraitGenetics GmbH (http://www.traitgenetics.com).

w7984_meraculous_scaffolds

Mascher, Martin (2014)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
Whole-genome shotgun of hexaploid wheat Synthetic W7984. The assembly was done with meraculous (Chapman et al., 2011, PLOS ONE) and consists of 6,870,110 scaffolds. The cumulative size of all scaffolds is 9,134,017,866 base pairs.

Beta vulgaris spp. maritima draft genome sequence assembly and structural prediction of protein coding genes

Himmelbauer, Heinz; Weisshaar, Bernd (2017)
Publisher: Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, Bielefeld, 33615, Germany
Dataset containing three files, namely contig and scaffold sequences (WB42_v2.fasta), an AGP file (WB42_v2.agp) to convert WB42_v2.fasta to a concatenated assembly version consisting of pseudochromosomes, and the result of a gene prediction performed with AUGUSTUS to describe Beta vulgaris spp. maritima protein coding genes, including genes which are not supported by mRNA evidence (WB42_v2.gff3).

Supplemental material : 'Isoprene emission-free poplars - a chance to reduce the impact from poplar plantations on the atmosphere

Schnitzler, Jörg-Peter (2014)
Publisher: Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
Depending on the atmospheric composition, isoprene emissions from plants can have a severe impact on air quality and regional climate. For the plant itself, isoprene can enhance stress tolerance and also interfere with the attraction of herbivores and parasitoids. Here, we tested the growth performance and fitness of Populus á canescens in which iso-prene emission had been knocked down by RNA interference technology (PcISPS-RNAi plants) for two growing seasons under ou...

Functional annotation of SNPs and INDELs from 52 highly diverse accessions of the model allopolyploid plant Brassica napus.

Schmutzer, Thomas (2015)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
This data resource contains the functional annotation of SNPs and INDELs for 52 Brassica napus lines. The analyzed sequence data was produced in the frame of the PreBreed-Yield project and was published (Snowdon et al. 2015, DOI: 10.1016/j.tplants.2015.04.013). The complete whole-genome shotgun resequencing data is archived at the European Nucleotide Archive (http://www.ebi.ac.uk/ena) under the project numbers PRJEB5974 and PRJEB6069. The discovery of INDELs is based on a gapped a...

Three-dimensional model of airspaces in the developing Brassica napus seed

Verboeven, Pieter (2012)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
Whole rapeseeds were scanned using a high resolution X-ray micro-CT system. Out of the reconstructed cross-section images (1500 virtual sections), the three-dimensional model of the void network in the developing seed of Brassica napus was generated. Developmental stage corresponds to the main storage phase (about 30 days after fertilization).

Data Management Experiences and Best Practices from the Perspective of a Plant Research Institute

Arend, Daniel (2014)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
Presentation on the DILS 17.July.2014 in Lisbon, Portugal