A scalable and responsive genomic data management system from GOBii. The mission of the Genomics Open-source breeding informatics initiative (GOBii) is to build open-source genomic data management and analysis tools to enable breeders to implement genomic and marker-assisted selection as part of their routine breeding programs.

1. RP Genetic Gains meeting
Jan 5-6, 2021
Himabindu Kudapa
Forward Breeding

2. GOBII Data Loader and Extractor

3. Experimental
design
Capture Collate/
organize
Curate AnalyzeArchive
Planting and
labeling in field
DNA Assay 38474037 38668738 38748270 38867490 MSU7_12_17391484_G/TMSU7_12_17391872_A/GMSU7_2_10003379_C/A
Plate 01-A01 G:G G:G T:T T:T T:T A:A A:A
Plate 01-A02 G:G G:G T:T T:T T:T A:A C:A
Plate 01-A03 G:G G:G T:T T:T T:T A:A C:A
Plate 01-A04 A:G A:G C:T G:T T:T A:A C:A
Plate 01-A05 A:G A:G C:T G:T T:T A:A C:C
Plate 01-A06 A:A A:A C:C G:G T:T A:A A:A
Plate 01-A07 A:G A:G C:T G:T T:T A:A C:C
Plate 01-A08 A:G A:G C:T G:T T:T A:A C:A
Plate 01-A09 A:A A:A C:C G:G T:G A:A A:A
Plate 01-A10 G:G G:G T:T T:T T:T A:A C:A
Plate 01-A11 A:A A:A C:C G:T T:T A:A A:A
Plate 01-A12 A:G A:G C:T G:T T:G A:A C:A
Plate 01-B01 A:G A:G C:T G:T T:T A:A C:A
Plate 01-B02 G:G G:G T:T T:T T:T A:A C:A
Plate 01-B03 A:A A:A C:C G:G T:T A:A C:A
Plate 01-B04 G:G G:G T:T T:T T:T A:A C:A
Plate 01-B05 A:A A:A C:C G:G T:T A:A C:C
Plate 01-B06 A:G A:G C:T G:T T:T A:A C:A
Plate 01-B07 A:A A:A C:C G:G T:T A:A C:C
Plate 01-B08 A:A A:A C:C G:G T:T A:A C:A
Plate 01-B09 A:A A:A C:C G:G T:T A:A A:A
Order form
Genotyping
data
BMS - GOBii - HTPG Integration
• Notify Intertek of upcoming orders
• Assign plate and sample IDs
• Provide barcodes
• Load raw data into GOBII
• Store genotypic data
• Facilitate data extraction
• Genotypic data in ready-to-
analyze formats
Connect data to
visualization and
analysis tools
HTPG

4. Flapjack for MABC
Goal: Identify the best individual plants in a
backcross population to cross or advance to
the next generation
Load genotypic data for the BC plants, the
donor, recurrent parents and the QTL file
Run the Marker-assisted backcrossing analysis
Load genotypic data for the F1 progeny and
their expected parents
Run the Pedigree Verification analysis:
F1 (known parents)
Pedver for F1 Pedigree Verification
Goal: Validate crosses
GOBii Tools

5. GOBii GS-Galaxy analysis pipeline

6. Genomic selection analysis pipeline
4. Visualize and select based on
prediction values
2. Get data by uploading from local or
browsing file from a server
5. Save Galaxy Workflow
1. GOBII data extract post to Galaxy
3. Run BGLR calculator by specifying parameters and models

7. GOBii community, collaboration and training
Workshop by the EiB with GOBii and HTPG
Uganda (November 8th-10th, 2017)
We are building a global community of
knowledge through workshops, hackathons
and cross-training to transform breeding
http://cbsugobii05.tc.cornell.edu/wordpress/

8. Genomic Prediction in Sorghum
VNMKV,
Parbhani
PDKV,
Akola
• Training population (~423 lines) encompassing parent material
for all important traits and varieties/ lines/ hybrids from NARS
(both from India and Africa) which include A and B lines, A2, A3
and A4 hybrids etc. customized
• Participation of two AICSIP centres - Parbhani, Akola
• Multi-location (3 locations) and 3 seasons data: Phenotyping for
morphological and agronomical traits along with key traits for
tolerance/resistance
• Preliminary data analysis of four major traits (including grain
yield) has been used to build-up six genomic prediction models
and identified three best models for sorghum breeding GS optimization and
sorghum breeding trial at Patancheru

9. In summary…
 Genomic resources available
 GOBii will serve as the repository for all genotyping data generated from
different projects
 Modernization of breeding program- use of decision support tools
 Forward breeding to enhance selection intensity with reduced genotyping cost
 Enhance user interface for better decision making