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15 research data, page 1 of 2

Technical validation experiment for reproducibility of high throughput plant phenotyping using LemnaTec automated image acquisition and IAP image analysis workflow

Astrid Junker, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany (2016)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
This dataset describes and quantifies the repeatability of the phenotyping workflow for the LemnaTec facility. Three single Arabidopsis thaliana plants in different developmental stages haven been subjected to repeated imaging over 50 rounds. The evaluation of geometric features extracted from the images using IAP and statistical post-processing revealed a high stability and reproducibility of the established imaging and analysis procedures.

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

Thomas, Schmutzer, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany (2015)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt 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 a VCC >= 2....

A Preliminary Review of Allium subg. Melanocrommyum in Central Asia

Reinhard M. Fritsch, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany (2016)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt 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. In the Taxono...

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), Stadt 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-ray attenuat...

w7984_meraculous_scaffolds

Martin Mascher, IPK Gatersleben, Corrensstraße 3, Stadt Seeland OT Gatersleben, D-06466, Germany (2014)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt 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.

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 outdoor conditions. Neithe...

Phenotypic data of seven quality traits for a population of Central European wheat hybrids and their parental inbred lines

Guozheng Liu, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany (2016)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
This data resource contains the Best Linear Unbiased Estimates of 135 elite winter wheat (Triticum aestivum L.) lines adapted to Central Europe and 1,604 F1 hybrids derived from them. All genotypes were evaluated for seven quality traits in up to six environments (Zhao et al. 2015; Proceedings of the National Academy of Sciences of the United States of America 112:15624-15629; DOI: 10.1073/pnas.1514547112; Liu et al. 2016. Liu et al. 2016; PlosOne; DOI: 10.1371/journal.pone.0158635). The sedi...

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

Thomas, Schmutzer, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany (2015)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt 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 alignment tha...

Repeat investigation of 4.3 million variant positions using 52 highly diverse accessions of the model allopolyploid plant Brassica napus.

Thomas, Schmutzer, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany (2015)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
The B. napus Darmor-bzh genome assembly contains 34.5% transposable elements. We performed a repeat investigation for all 4.3 million determined variant positions (DOI:10.5447/IPK/2015/5). All variant positions (VPs) were compared to known repeat positions, given in the GFF annotation (v5) file of the B. napus Darmor-bzh reference (Chalhoub et al. 2014, DOI: 10.1126/science.1253435). In addition a k-mer analysis was performed to provide further insights of the repeat constitution in our genot...

Raw images files from quantitative monitoring of 484 Arabidopsis thaliana plants using high-throughput plant phenotyping

Astrid Junker, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany (2016)
Publisher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
This dataset contains 30426 raw image files from a high-throughput plant phenotyping experiment. The growth and development of 484 Arabidopsis thaliana plants (C24 genotype) in respect to plant movement and soil cover has been monitored over 55 days. The files are described using the ISA-Tab format and fulfill the MIAPPE recommendations.