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 M. Bassi; Ousmane Boukar; Douglas Cook; Alan Cruickshank; Christian Fatokun; Noureddine El Haddad; Alan Humphries; David Jordan; Zacharia Kehel; Shiv Kumar; Sandy Jan Labarosa; Loi Huu Nguyen; Emma Mace; Susan McCouch; Ken McNally; David F. Marshall; Erick Owuor Mikwa; Iain Milne; Damaris Achieng Odeny; Mariola Plazas; Jaime Prohens; Loren H. Rieseberg; Roland Schafleitner; Shivali Sharma; Gordon Stephen; Huynh Quang Tin; Abou Togola; Emily Warschefsky; Peter Werner; All our CWR Pre-Breeding Partners and Collaborators; Paul D. Shaw

doi:10.1002/csc2.20248

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 M. Bassi, Ousmane Boukar, Douglas Cook, Alan Cruickshank, Christian Fatokun, Noureddine El Haddad, Alan Humphries, David Jordan, Zacharia Kehel, Shiv Kumar, Sandy Jan Labarosa, Loi Huu Nguyen, Emma Mace, Susan McCouch, Ken McNally, David F. MarshallErick Owuor Mikwa, Iain Milne, Damaris Achieng Odeny, Mariola Plazas, Jaime Prohens, Loren H. Rieseberg, Roland Schafleitner, Shivali Sharma, Gordon Stephen, Huynh Quang Tin, Abou Togola, Emily Warschefsky, Peter Werner, All our CWR Pre-Breeding Partners and Collaborators, Paul D. Shaw^*

^*Corresponding author for this work

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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.

Original language	English
Pages (from-to)	1538-1566
Number of pages	29
Journal	Crop Science
Volume	61
Issue number	3
Early online date	20 Aug 2020
DOIs	https://doi.org/10.1002/csc2.20248
Publication status	First published - 20 Aug 2020

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csc2.20248Final published version, 2.55 MBLicence: CC BY-NC-ND

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Raubach, S., Kilian, B., Dreher, K., Amri, A., Bassi, F. M., Boukar, O., Cook, D., Cruickshank, A., Fatokun, C., El Haddad, N., Humphries, A., Jordan, D., Kehel, Z., Kumar, S., Labarosa, S. J., Nguyen, L. H., Mace, E., McCouch, S., McNally, K., ... Shaw, P. D. (2020). From bits to bites: Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives. Crop Science, 61(3), 1538-1566. Advance online publication. https://doi.org/10.1002/csc2.20248

@article{5a0354ff52b44ae096715f5741a84afa,

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

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 {\textquoteleft}Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives{\textquoteright} (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.",

author = "Sebastian Raubach and Benjamin Kilian and Kate Dreher and Ahmed Amri and Bassi, {Filippo M.} and Ousmane Boukar and Douglas Cook and Alan Cruickshank and Christian Fatokun and {El Haddad}, Noureddine and Alan Humphries and David Jordan and Zacharia Kehel and Shiv Kumar and Labarosa, {Sandy Jan} and Nguyen, {Loi Huu} and Emma Mace and Susan McCouch and Ken McNally and Marshall, {David F.} and Mikwa, {Erick Owuor} and Iain Milne and Odeny, {Damaris Achieng} and Mariola Plazas and Jaime Prohens and Rieseberg, {Loren H.} and Roland Schafleitner and Shivali Sharma and Gordon Stephen and Tin, {Huynh Quang} and Abou Togola and Emily Warschefsky and Peter Werner and {All our CWR Pre-Breeding Partners and Collaborators} and Shaw, {Paul D.}",

year = "2020",

month = aug,

day = "20",

doi = "10.1002/csc2.20248",

language = "English",

volume = "61",

pages = "1538--1566",

journal = "Crop Science",

issn = "0011-183X",

publisher = "Crop Science Society of America",

number = "3",

}

Raubach, S, Kilian, B, Dreher, K, Amri, A, Bassi, FM, Boukar, O, Cook, D, Cruickshank, A, Fatokun, C, El Haddad, N, Humphries, A, Jordan, D, Kehel, Z, Kumar, S, Labarosa, SJ, Nguyen, LH, Mace, E, McCouch, S, McNally, K, Marshall, DF, Mikwa, EO, Milne, I, Odeny, DA, Plazas, M, Prohens, J, Rieseberg, LH, Schafleitner, R, Sharma, S, Stephen, G, Tin, HQ, Togola, A, Warschefsky, E, Werner, P, All our CWR Pre-Breeding Partners and Collaborators & Shaw, PD 2020, 'From bits to bites: Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives', Crop Science, vol. 61, no. 3, pp. 1538-1566. https://doi.org/10.1002/csc2.20248

TY - JOUR

T1 - From bits to bites

T2 - Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives

AU - Raubach, Sebastian

AU - Kilian, Benjamin

AU - Dreher, Kate

AU - Amri, Ahmed

AU - Bassi, Filippo M.

AU - Boukar, Ousmane

AU - Cook, Douglas

AU - Cruickshank, Alan

AU - Fatokun, Christian

AU - El Haddad, Noureddine

AU - Humphries, Alan

AU - Jordan, David

AU - Kehel, Zacharia

AU - Kumar, Shiv

AU - Labarosa, Sandy Jan

AU - Nguyen, Loi Huu

AU - Mace, Emma

AU - McCouch, Susan

AU - McNally, Ken

AU - Marshall, David F.

AU - Mikwa, Erick Owuor

AU - Milne, Iain

AU - Odeny, Damaris Achieng

AU - Plazas, Mariola

AU - Prohens, Jaime

AU - Rieseberg, Loren H.

AU - Schafleitner, Roland

AU - Sharma, Shivali

AU - Stephen, Gordon

AU - Tin, Huynh Quang

AU - Togola, Abou

AU - Warschefsky, Emily

AU - Werner, Peter

AU - All our CWR Pre-Breeding Partners and Collaborators

AU - Shaw, Paul D.

PY - 2020/8/20

Y1 - 2020/8/20

N2 - 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.

AB - 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.

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U2 - 10.1002/csc2.20248

DO - 10.1002/csc2.20248

M3 - Article

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EP - 1566

JO - Crop Science

JF - Crop Science

IS - 3

ER -

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

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