Solgenomics conference talk 2018, Mueller lab

1. Breeding Informatics
Solutions at SGN
(solgenomics.net)
Isaak Yosief Tecle
Mueller Lab
Boyce Thompson Institute, Ithaca, NY

3. Overview
n Database
n Large scale, high dimension
n Field work tools
n Trial design and data collection
n Analysis tools
n Exploratory and inferential

4. Towards a one-stop digital
ecosystem

5. Why it is necessary?
n High-throughput data
n Access, sharing, security
n Multiple partners
n Efficiency, data integrity, result reproducibility
n Integrated data collection and analysis
tools
n Data validation
n Automation of repetitive tasks
n Knowledge discovery
n Internal and external cross-references

6. SGN: Accessible from any device…

8. Ontology

10. § Links QTLs to
annotated
genomes and
genetic maps

11. YourCropBase.org
‘Half-sib’ databases…

12. Register genetic material
Accessions
Populations
Crosses and progenies
Seedlot

13. Register crosses and progenies

14. Design genotyping plates

15. Register seedlot

17. View pedigree

18. Field work tools

19. Design trials

20. Barcode observation units

21. Collect data: FieldBook app
• Trial layout
• Traits
• Phenotype
data

23. Exploratory tools

25. Filter interactively

26. Compare traits across trials

27. Analysis tools

28. Check traits correlation

29. Run ANOVA

30. Calculate selection index

31. Check population structure (PCA)…

32. Create groups (clusters)

33. Genomic Selection Tool
(solGS)
Tecle et. al. (2014) BMC Bioinformatics 15:398

34. Create a training dataset

40. Accessing and downloading
data

42. Summary
Genetic material
Ontologies
Trial data
Data repository Data exploring
and analysis
Phenotype & genotype
collection tools
User-Friendly
interface

43. Sponsors and collaborators

44. n solgenomics.net/contact/form/
n Here:
n Lukas
n Suzy
n Isaak
n Demo: Cassavabase.org
Thank You!