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Data overload – Breeding decision-support software to the rescue !

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  1. Data overload – Breeding decision-support software to the rescue! S. Jung, Taein Lee, Kate Evans, Cameron Peace, Gennaro Fazio, SushanRu, Amy F. Iezzoni, Doreen Main

  2. Outline of Presentation • BIMS (Breeding Information Management System) – what is it? • Why BIMS? • What data does BIMS have? • What features are in BIMS? • Testimonials • BIMS for your crop! RosBREED

  3. What is BIMS? BIMS Breeding Information Management System Functionality Web portal that leverage genomics information for maximum utility within the Marker-Assisted Breeding (MAB) Pipeline, including functions to aid breeding decision-making Where is it? Integrated with GDR (Genome database for Rosaceae) that contains genomic, genetic and breeding data RosBREED

  4. Why BIMS? Genotypic data, phenotypic data – Too much to handle! Which parents to cross? Which seedlings to select? Which QTLs to try to adapt to my breeding program? RosBREED

  5. With BIMS we can help you with what trees to cross RosBREED

  6. What data does BIMS have? Breeding Data from participating RosBREEDbreeders (apple, strawberry, tart cherry, sweet cherry and peach) Phenotypic data, genotypic data, pedigree data, germplasm data, etc Integrated with other GDR genetics and genomics data markers, QTL, genetic map, whole genome sequences, trait ontology RosBREED

  7. What features are in BIMS? • Comprehensive search site for breeding data • Modules to support MAB pipeline RosBREED

  8. Database for breeding data • Browse by dataset • Search phenotypic data • Search genotypic data • Generate input file for software (Pedimap, FlexQTL)

  9. Phenotypic data search

  10. Variety Detail Page

  11. Genotypic data search

  12. Tools – Generate Input files for Pedimap, a breeding software

  13. Modules to support MAB pipeline RosBREED

  14. Trait Locus Warehouse

  15. Selection Target Identifier • Fresh market • Processing market • … Choose market class See SE Values mock-up only

  16. Select Target Identifier Choices Made Trait 2 Trait 1 Trait Name Sweetness Acidity Statistical Significance of QTL BF 21.3 mock-up only LOD 7.6 Market Type Fresh Fresh Print Search Result User can rewrite these values Reset

  17. Technology Portfolio

  18. Genome Database Resources Graphical location of chosen QTL LG1 LG2 LG3 LG4 LG5 If better marker is necessary, look up to find SSRs and SNPS around QTL and design primers using online software Zoom in on QTL interval and discover what markers are there to be utilized for MAS x o mock-up only o

  19. Reference Germplasm Database • A module to help a breeder to become convinced or otherwise that an unproven DNA test of interest indeed holds predictive power for germplasm of interest. • Simple Validation • Functional genotype effects RosBREED

  20. Cross Assist Generates a list of parents and the number of seedlings to get the progeny with desired traits

  21. A RosBREED Tart Cherry breeder Amy Iezzoni says.. • “I really like having my breeding data searchable from a web portal. No more pouring over spreadsheets hoping I have the latest one, looking for a particular data point! With the toolbox, I can just log in and search for the data point and have it in a matter of minutes.” RosBREED

  22. A RosBREEDApple breeder Jim Luby says.. • “I like the searchable database format for my potential parents and the ability to get a Pedimap-ready output without the worry about format is really efficient for visualizing phenotypes in our breeding program.” RosBREED

  23. A RosBREEDStrawberry breeder Jim Hancock says.. “To date, I have done all my evaluations and parent selection by shuffling through spread sheets and hand written notes. I hope to streamline my whole operation with BIMS.” RosBREED

  24. A RosBREEDApple breeder Kate Evans says.. “Being able to search through multiple years of phenotypic data as well as link in genotypic data is wonderful. I can easily make selections and chose potential parents using the Toolbox format.” RosBREED

  25. BIMS for your crop group • Underlying database for BIMS is constructed using Chado, an open-source, generic, modular, ontology-based database for biological data • BIMS is developed by the collaboration between breeders, geneticists, genomicists, and bioinformaticists • Can be applicable for any other crops, not just for Rosaceae RosBREED

  26. Acknowledgement • BIMS team • Team Leader: Gennaro Fazio • BIMS module design team: Cameron Peace, Gennaro Fazio, SushanRu • BIMS database designer: Sook Jung • BIMS Database developer: Taein Lee • BIMS Trainee: SushanRu • Genomics Team Leader/ GDR : Dorrie Main • MAP Pipeline Team Leader: Cameron Peace • Other RosBREED Team Members • PD: Amy Iezzoni • Kate Evans (Design of breeding database) • Breeding team who provided data This project is supported by the Specialty Crop Research Initiative of USDA’s National Institute of Food and Agriculture