BRIDGE – A Visual Analytics Web Tool for Barley Genebank Genomics

König, Patrick; Beier, Sebastian; Basterrechea, Martín; Schüler, Danuta; Arend, Daniel; Mascher, Martin; Stein, Nils; Scholz, Uwe; Lange, Matthias

doi:10.3389/fpls.2020.00701

Cited by 33 publications

(23 citation statements)

References 65 publications

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“…For wheat improvement, extensive genetic diversity comprising advanced cultivars, breeding lines, traditional cultivars and landraces, genetic stocks, introgression lines, mutants, and CWR is conserved ex situ in genebanks worldwide. According to the Food and Agriculture Organization (FAO) World Information and Early Warning System (WIEWS) Such platforms include Germinate [64,65](https://ics.hutton.ac.uk/get-germinate accessed on 21 September 2021), Legume Information system [66](https://legumeinfo.org accessed on 21 September 2021), and BRIDGE [67], which provide access to detailed experimental and trial data for subsets of germplasm that may or may not be held within the genebank system [64]. In addition, supporting organizations (institutions, universities, and private companies) have germplasm information that may be publicly available, even if it is not included in the core platforms.…”

Section: Status Of the Wheat Germplasm Conserved Ex Situmentioning

confidence: 99%

Introducing Beneficial Alleles from Plant Genetic Resources into the Wheat Germplasm

Sharma¹,

Schulthess

Bassi³

et al. 2021

Biology

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Wheat (Triticum sp.) is one of the world’s most important crops, and constantly increasing its productivity is crucial to the livelihoods of millions of people. However, more than a century of intensive breeding and selection processes have eroded genetic diversity in the elite genepool, making new genetic gains difficult. Therefore, the need to introduce novel genetic diversity into modern wheat has become increasingly important. This review provides an overview of the plant genetic resources (PGR) available for wheat. We describe the most important taxonomic and phylogenetic relationships of these PGR to guide their use in wheat breeding. In addition, we present the status of the use of some of these resources in wheat breeding programs. We propose several introgression schemes that allow the transfer of qualitative and quantitative alleles from PGR into elite germplasm. With this in mind, we propose the use of a stage-gate approach to align the pre-breeding with main breeding programs to meet the needs of breeders, farmers, and end-users. Overall, this review provides a clear starting point to guide the introgression of useful alleles over the next decade.

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Section: Status Of the Wheat Germplasm Conserved Ex Situmentioning

confidence: 99%

Introducing Beneficial Alleles from Plant Genetic Resources into the Wheat Germplasm

Sharma¹,

Schulthess

Bassi³

et al. 2021

Biology

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“…We have integrated isa4j into the BRIDGE portal, which is a visual analytics and data warehouse web application hosting data of 22621 genotyped and 9527 phenotyped germplasm samples of barley ( Hordeum vulgare L.) 12 . The underlying data was derived from the study of Milner et al 13 .…”

Section: Resultsmentioning

confidence: 99%

isa4j: a scalable Java library for creating ISA-Tab metadata

et al. 2020

Self Cite

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Experimental data is only useful to other researchers if it is findable, accessible, interoperable, and reusable (FAIR). The ISA-Tab framework enables scientists to publish metadata about their experiments in a plain text, machine-readable format that aims to confer that interoperability and reusability. A Python software package (isatools) is currently being developed to programmatically produce these metadata files. For Java-based environments, there is no equivalent solution yet. While the isatools package provides a lot of flexibility and a wealth of different features for the Python ecosystem, a package for JVM-based applications might offer the speed and scalability needed for writing very large ISA-Tab files, making the ISA framework available in an even wider range of situations and environments. Here we present a light-weight and scalable Java library (isa4j) for generating metadata files in the ISA-Tab format, which elegantly integrates into existing JVM applications and especially shines at generating very large files. It is modeled after the ISA core specifications and designed in keeping with isatools conventions, making it consistent and intuitive to use for the community. isa4j is implemented in Java (JDK11+) and freely available under the terms of the MIT license from the Central Maven Repository (https://mvnrepository.com/artifact/de.ipk-gatersleben/isa4j). The source code, detailed documentation, usage examples and performance evaluations can be found at https://github.com/IPK-BIT/isa4j.

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“…A FAIR principle [ 46 ] compliant data management is currently under development. The pipeline follows the basic schema of the BRIDGE Visual Analytics Web Tool for Barley Genebank Genomics [ 47 ]. It will allow visualization and export of the phenotypic and genotypic data, online GWAS, and several other features of interest to the scientist and plant breeders.…”

Section: Discussionmentioning

confidence: 99%

“Macrobot”: An Automated Segmentation-Based System for Powdery Mildew Disease Quantification

et al. 2020

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Managing plant diseases is increasingly difficult due to reasons such as intensifying the field production, climatic change-driven expansion of pests, redraw and loss of effectiveness of pesticides, rapid breakdown of the disease resistance in the field, and other factors. The substantial progress in genomics of both plants and pathogens, achieved in the last decades, has the potential to counteract this negative trend, however, only when the genomic data is supported by relevant phenotypic data that allows linking the genomic information to specific traits. We have developed a set of methods and equipment and combined them into a “Macrophenomics facility.” The pipeline has been optimized for the quantification of powdery mildew infection symptoms on wheat and barley, but it can be adapted to other diseases and host plants. The Macrophenomics pipeline scores the visible powdery mildew disease symptoms, typically 5-7 days after inoculation (dai), in a highly automated manner. The system can precisely and reproducibly quantify the percentage of the infected leaf area with a theoretical throughput of up to 10000 individual samples per day, making it appropriate for phenotyping of large germplasm collections and crossing populations.

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BRIDGE – A Visual Analytics Web Tool for Barley Genebank Genomics

Cited by 33 publications

References 65 publications

Introducing Beneficial Alleles from Plant Genetic Resources into the Wheat Germplasm

Introducing Beneficial Alleles from Plant Genetic Resources into the Wheat Germplasm

isa4j: a scalable Java library for creating ISA-Tab metadata

“Macrobot”: An Automated Segmentation-Based System for Powdery Mildew Disease Quantification

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