From bits to bites: Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives

Sebastian Raubach, Benjamin Kilian, Kate Dreher, Ahmed Amri, Filippo Bassi, Ousmane Boukar, Douglas Cook, Alan Cruickshank, Christian Fatokun, Noureddine El Haddad, Alan Humphries, David Jordan, Zakaria Kehel, Shiv Kumar Agrawal, Sandy Jan Labarosa, Loi Huu Nguyen, Emma Mace, Susan McCouch, Kenneth L. McNally, David F. Marshall, Erick Mikwa, Iain Milne, Damaris Odeny, Mariola Plazas, Jaime Prohens, Loren H. Rieseberg, Roland Schafleitner, Shivali Sharma, Gordon Stephen, Huynh Quang Tin, Abou Togola, Emily Warschefsky, Peter Werner, Paul Shaw. (30/6/2020). From bits to bites: Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives. Crop Science, pp. 1-29.

Abstract

Management and distribution of experimental data from prebreeding projects is important to ensure uptake of germplasm into breeding and research programs. Being able to access and share this data in standard formats is essential. The adoption of a common informatics platform for crops that may have limited resources brings economies of scale, allowing common informatics components to be used across multiple species. The close integration of such a platform with commonly used breeding software, visualization, and analysis tools reduces the barrier for entry to researchers and provides a common framework to facilitate collaborations and data sharing. This work presents significant updates to the Germinate platform and highlights its value in distributing prebreeding data for 14 crops as part of the project ‘Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives’ (hereafter Crop Trust Crop Wild Relatives project) led by the Crop Trust (https://www.cwrdiversity.org). The addition of data on these species compliments data already publicly available in Germinate. We present a suite of updated Germinate features using examples from these crop species and their wild relatives. The use of Germinate within the Crop Trust Crop Wild Relatives project demonstrates the usefulness of the system and the benefits a shared informatics platform provides. These data resources provide a foundation on which breeding and research communities can develop additional online resources for their crops, harness new data as it becomes available, and benefit collectively from future developments of the Germinate platform.