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W613: The genomic open-source breeding informatics initiative: Developing a global community of knowledge surrounding the use of markers in genomic selection

Jones, E., Robbins, K., Gao, S.Y., Nti-Addae, Y.A., Dreher, K.A., Olsen, M., Dreisigacker, S., Varshney, R.K.ORCID: 0000-0002-4562-9131, Rathore, A., Cobb, J.N., Maulen, R. and McCouch, S. (2019) W613: The genomic open-source breeding informatics initiative: Developing a global community of knowledge surrounding the use of markers in genomic selection. In: Plant & Animal Genome Conference XXVII, 12 - 16 January 2019, San Diego, CA


The Genomic Open-Source Breeding informatics initiative (GOBii) is a Bill and Melinda Gates funded project with the mission to implement genomic and marker assisted selection as part of routine breeding programs for staple crops at CGIAR centers. We believe that much of the gains that have been achieved by major ag-biotech companies can also be achieved in these centers through adopting data management systems and bioinformatics pipelines that aid breeding decisions. Our challenge is to implement genomics data management and connect to breeding data management and analysis tools being developed as part of diverse projects and within different organizational structures. To achieve our goal, we have employed a global team of data curators, developers, molecular breeders and system administrators based at Cornell University, The Boyce Thompson Institute and at each of our collaborating CGIAR centers; CIMMYT, ICRISAT and IRRI. This team have experience and skill sets that cross multiple data management and curation projects with backgrounds in industry and academia and together can collaborate to find best solutions for use cases gathered in their own environments. We are partnering synergistically with adjacent data management and genotyping projects to prevent feature redundancy and promote the use of data management systems, and we are aligned with the Excellence in Breeding Program to ensure united approaches and goals. Our CGIAR center partners have now become the experts in managing and analyzing genomics and genotyping data and are training their own communities in using these systems. Together we have built Genomic Selection pipelines in Galaxy, data QC tools with Diversity Arrays Technologies and marker-assisted backcrossing, forward breeding and pedigree verification with the James Hutton Institute, based on use cases collected by our CGIAR molecular breeders. Together we are building a global community of knowledge surrounding best practices for implementing marker-assisted and genomic selection at CGIAR centers.

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