Germinate 3: Development of a Common Platform to Support the Distribution of Experimental Data on Crop Wild Relatives

Abstract

Conservation and exploitation of crop wild relative species is an important component in ensuring food security and improving current agricultural output. By identifying agriculturally important characteristics that express favorable response to both biotic and abiotic stress currently unused by breeders, the incorporation of this new genetic material into genetic background stocks may help mitigate problems imposed by climate change, land degradation, and population pressure. This is particularly important in countries that will be more severely affected by the threat of reduced yields. The ability to effectively manage genetic resources collections and integrate unique and diverse data types is crucial in exploring, understanding, and exploiting the diversity contained within genebanks. Providing a common interface through which experimental and background data can be disseminated to both researchers and breeders will bring focus and facilitate community building into research communities. We have taken wild barley (Hordeum spp.) and potato (Solanum spp.) collections along with wheat (Triticum spp.) and maize (Zea mays subsp. mays) and their wild relatives and incorporated this data into web‐based information resources built using the Germinate platform (https://ics.hutton.ac.uk/get-germinate, accessed 4 Apr. 2017). We have tailored these to better meet the demands of researchers by developing both new data visualization tools and integration with current software such as Helium, Flapjack, and CurlyWhirly (https://ics.hutton.ac.uk/software, accessed 4 Apr. 2017) and presented the data in a common platform. While the underlying species differ, the approach taken ensures that tools are compatible across all database instances. We will describe these database instances and show that Germinate offers a common platform that will aid in the exploration and wider use of these species.

Development and Evaluation of a Barley 50k iSelect SNP Array

“…An online resource was developed to store background data such as the SNP source sequence, locus name, sequence orientation, SNP effects data and any additional information known on each locus. This resource is based on the Germinate data infrastructure (Shaw et al, 2017 ) and allows users to search and retrieve background design information for each SNP (49,267 in total) on the barley 50k SNP array. Users can search for individual marker names to retrieve additional information or download the entire dataset for browsing in text or Excel.…”

BRIDGE – A Visual Analytics Web Tool for Barley Genebank Genomics

“…One application framework for which a barley instance is available is Germinate3 (Shaw et al, 2017). Compared to BRIDGE, it shares some of the features and behaves more like a traditional table-based data warehouse than a visual analytics driven application.…”

Wheat genetic resources in the post-genomics era: promise and challenges

“…Considerable investment in data management and informatics systems will be required to ensure that gene banks can fulfil their roles as custodians of the expanding genetic knowledge linked to their physical resources. This view was echoed by Shaw et al (2017), who reported that the ability to effectively manage genetic resource collections and integrate unique and diverse data types is crucial in exploring, understanding and exploiting the diversity contained within gene banks. A 'one shoe fits all' approach that promotes a common platform may negate the achievement of that goal.…”