Cassavabase-PhenoApps demo ISTRC 2018
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This document summarizes a presentation on breeding data management and analysis tools using the Cassavabase database. It describes how Cassavabase collects phenotypic and genotypic data from various programs and ensures data quality. Over 9 million phenotypic observations, 2488 trials and 34,000 genotypes have been collected. It also discusses expanding interoperability through APIs and partnerships with other crop databases. The presentation demonstrates using Cassavabase to access trial data, visualize genotypes, perform statistical analysis, genomic prediction and multi-trait selection to increase genetic gain.
Cassavabase-PhenoApps demo ISTRC 2018
- 1. Palmira, October 2018 Mueller lab demoand Guillaume Bauchet, Bryan Ellerbrock, David Lyon, Naama Menda, Nicolas Morales, Alex C. Ogbonna, Adrian Powell, Titima Tantikanjana and Isaak Y Tecle
- 2. Mueller lab - Bioinformatics - Genomics - Databases https://btiscience.org/lukas-mueller/#lab-members https://www.facebook.com/solgenomics/
- 4. Ensuring Data Quality • Integrated electronic data capture using the Android Fieldbook and other tablet-based solutions • Digital data never “leaks” into “analog” domain • Widely used barcoding ensures data collection quality • Quality filtering upon upload
- 5. Cassavabase Status • Has collected breeding data from all NextGen programs • 9.7 million phenotypic observations • 2488 trials • 34,000 genotypes • From phase I (2012-2017) to phase II (2018-2022): • Increase data collection and ensure quality • Increase database interoperability and expand the “digital ecosystem” to farmers
- 8. Expanding resources: BrAPI • Breeding Application Programming Interface (API) • Language support: Brapi.R interface and Brapi.JS • Data exchange • New way for coding breeding applications (BrAPPs) • BrAPPs run on any data backend that supports BrAPI cassavabase BMS GOBii Flapjack Germinate B4R = Empower breeder’s toolbox to increase genetic gain https://github.com/CIP-RIU/brapi
- 10. Today’s Demo Content 3.00-4.00: Breeding Data Management, Sample Tracking and FieldApp (Guillaume) 4.00-5.00: Data analysis (Isaak)
- 11. User: sgn Password: eggplant 1: Generic password: Database training websites https://cassava-test.sgn.cornell.edu/
- 12. https://cassava-test.sgn.cornell.edu/ 2: Personal password: User: breeder1, breeder2,…,breeder10 Password: ISTRC18
- 13. Account Privileges Account Type Privileges none Browse, use tools “user" User database, forum “submitter" create trials, add phenotype information etc. “Curator” All previous + data deletions
- 14. Create New Trial Fieldbook files Creation Collect Data & samples Import and Setup Trial in PhenoApps Upload Phenotypes Historical data Uploads Phenotype/ Genotype Analysis Crossings & Nursery Search/Download accessions-seeds Manage -> List -> Dataset Manage data collection -> barcode tools -> label design -> phenoApps Pedigree & Crossing -> cross upload -> seedlots -> phenoApps -> Selection Index -> Summary statistics -> Graphical filtering Search tools -> Single criteria -> Wizard search Select / add accessions Database pipeline and tools: the Big picture + Trait ontologies + SNP marker data -> ANOVA, HIDAP -> Trial comparison -> Genomic selection Analysis
- 15. Workflows
- 16. data collection workflow Phenotype data collection
- 17. Workflows
- 18. Tissue sampling data collection workflow Tutorial: https://www.slideshare.net/solgenomics/sample-tracking-tutorialistrc2018
- 19. https://cassava-test.sgn.cornell.edu/breeders/search -1- Select the “2018_NGCGOBII_Gstr ialdataset” -2- Click ”select all”: -3- Select ”traits” such as: fresh root yield|CO_334:0000013 top yield|CO_334:0000017 root number counting|CO_334:0000011 harvest index variable|CO_334:0000015 dry matter content by specific gravity method|CO_334:0000160 dry matter content percentage|CO_334:0000092 cassava mosaic disease severity 1-month evaluation|CO_334:0000191 cassava mosaic disease severity 3-month evaluation|CO_334:0000192 cassava mosaic disease severity 6-month evaluation|CO_334:0000194 -4- Download data in excel: -5- Store your selection as a dataset. It will be stored under your profile on cassavabase an can be re-accessed anytime (same as list) Access data from cassavabase
- 20. • Exploratory • Descriptive statistics • Interactive visualization • Pairwise multiple comparison • Inferential • ANOVA, correlation, population structure, clustering • Genomic Prediction • QTL analysis…coming soon • GWAS…coming soon
- 21. • Efficiency • Automation • Reproducibility • Access and sharing
- 27. Compare traits across trials
- 28. Analyze data
- 32. Run ANOVA
- 34. Check population structure (PCA)…
- 35. Partition samples into groups (clusters)
- 36. GWAS
- 37. GWAS
- 39. Phenotyped & genotyped individuals Genomic selection… Prediction model Predicted breeding Values (GEBVs) Genotyped selection candidates Training population
- 40. Prediction modeling • Univariate • Two-stage analysis • GBLUP • Marker-based realized relationship matrix • Prediction accuracy • Based on 2 replication, 10-fold cross-validation
- 42. Creating a training dataset
- 44. Fitting a prediction model
- 55. Estimating breeding values of selection candidates Applying the model…
- 58. Selection gain?
- 62. GEBVs based Multi-trait selection: Selection index
- 64. Summary • Exploratory and inferential analysis • Interactive visualization • Adds efficiency, reproducibility • Easy access and sharing
- 65. Contact us! USER MANUAL CONTACT SGN TEAM
- 67. Online manual: https://solgenomics.github.io/sgn/ Request new traits: http://submit.rtbbase.org/ Slides: http://www.slideshare.net/solgenomics Looking for code? Online Resources Looking for database tutorials or ontology request? Looking for phenoApps? PhenoApps: https://github.com/PhenoApps https://www.youtube.com/playlist?list=PLs7Y2nGwfz4E5_gv1H6Y4imeWDkFJDhIn Cassavabase code: https://github.com/solgenomics BrAPI code: https://brapi.org/ BrApps: https://brapi.org/brapps.php