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

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!

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

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?

With BIMS we can help you with what trees to cross

What data does BIMS have? Breeding Data from participating RosBREED breeders (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

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

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

Phenotypic data search 9

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Variety Detail Page

Genotypic data search 12

Tools – Generate Input files for Pedimap, a breeding software

Modules to support MAB pipeline

Trait Locus Warehouse

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

Acidity BF 21.3 Sweetness Trait 2 Trait 1 Market Type Select Target Identifier Choices Made Trait Name Statistical Significance of QTL LOD 7.6 Fresh QTL name TraitEffectStat. signif. Population/ germplasm SourceGenomic location Market type RangePriority index/EWL ocusV Glu7.1sweetn ess ±4BrixBF 23.1RosBREED CR Set Tex1342:37-43Fresh ±3 MDH3acidity± 0.32 mea LOD 7.6 Con × Bolinha Bolinha1:21.4Fresh8-105±1 Search Result Print Reset User can rewrite these values mock-up only

Technology Portfolio

Genome Database Resources LG1 LG2 LG3 LG4 LG5 Graphical location of chosen QTL Graphical location of chosen QTL Zoom in on QTL interval and discover what markers are there to be utilized for MAS QTL nameTraitEffect RangeGenomic Location/IntervalQTL origin infoGenomic Resources available near QTL SSC 4.5SSCLG4 – cMApple RosBREED flexQTLSSR1, SNP12343, SCAR abcd, …. TA 1.4TALG1 – cMFiestaxDiscovery cross SSC 4.2SSCLG4 – cM If better marker is necessary, look up to find SSRs and SNPS around QTL and design primers using online software mock-up only

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

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

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.

A RosBREED Apple 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.

A RosBREED Strawberry 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.

A RosBREED Apple 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.

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

Acknowledgement BIMS team Team Leader: Gennaro Fazio BIMS module design team: Cameron Peace, Gennaro Fazio, Sushan Ru BIMS database designer: Sook Jung BIMS Database developer: Taein Lee BIMS Trainee: Sushan Ru 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 USDAs National Institute of Food and Agriculture