Dr Rajeev K Varshney updated on the key points on Global open breeding informatics initiative project; Translating genomics information for crop improvement, Genomic resources and cost-effective genotyping platforms are made available with precise phenotyping, user friendly pipelines and decision support tools developed for use in Breeding programs.

1. Global open breeding informatics
initiative (GOBii)
Rajeev K Varshney

2. Translating genomics information
for crop improvement
Genomic resources and
cost-effective genotyping
platforms are made
available with precise
phenotyping
User friendly pipelines and
decision support tools
developed for use in
Breeding programs
Genomic
selection
MAS

3. GOBii goals
• Provide an open-source database to manage
genotyping data from multiple genotyping
platforms for any crop
• Provide user interfaces to query across datasets
by samples and markers
• Provide analyses and visualizing tools to support
data curation and breeding decisions
• Develop solutions to integrate GOBii with
adjacent breeding management, sample tracking,
vendor systems and downstream tools
• Provide consulting to manage data, and
implement genomic and marker-assisted
selection
• Develop a global community of developers, data
curators, molecular breeders and breeders with a
common interest to transform breeding

4. MID Breeders
Manish Roorkiwal
Prasad Bajaj Chaitanya SarmaS Sivasubramani
Principal Investigator
Rajeev K Varshney
Curators
Developers
Himabindu Kudapa Anilkumar V Roma R Das
IT Specialist
Pradyut Modi
Chickpea Breeder
S Srinivasan
Sorghum Breeder
C Bharadwaj
GOBII Team @ ICRISAT
M Govindaraj
Abhishek Rathore Anu ChitikineniSantosh Deshpande
Biometrician Genomicist Senior Manager

5. GOBii and System IntegrationGOBii-HTPG
Integration
GOBii Instances
@ICRISAT
GOBii Tools

6. 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/

7. Continuous needs assessment, prioritization
and feedback
• Release and onsite deployment of genomic database, Genomics Open Source Breeding Informatics
Initiative (GOBii)- v2.1 (Sep, 2019), improved versions of the GOBii v2.2 (March 7, 2020), v2.2.1 (July,
2020); and the latest version v2.2.2 (Oct, 2020)
• Data loaded on GOBii instances for ICRISAT mandate crops including peanut, pigenpea and pearl
millet, in addition to chickpea and sorghum.
• Uploaded a total of 16.32 billion datapoints for 5524 chickpea samples (three projects (3171 samples
& 3,941,492 marker, 195 samples & 19,574,878 markers and 2158 samples & 2014 markers)). One more
dataset of ~2800 samples with >2k markers being curated for uploading on GOBii database.
• Curation of additional 250 datasets for chickpea, groundnut and pigeonpea for uploading on GOBii.
• Data on 23 pigeonpea MABC populations; 9 historical data files on groundnut.
• Developed QC panel for chickpea and sorghum using WGS and high-density genotyping data on
parental lines from ICRISAT breeding programs.
• Chickpea QC panel with 14 SNPs developed and ready for deployment. Preliminary data on chickpea
QC panel for >17K datapoints (~370 samples and 48 markers) for QC development and >21K datapoints
(1504 samples and 14 markers) representing more than 90 breeding population from ICRISAT chickpea
breeding program uploaded after curation and available for breeder to make selection.

8. • Provided continuous feedback and inputs for FlapJack MABC
and F1 Ped Ver module.
• GOBii decision support tool, Genomic Selection - Galaxy
developed and is being deployed for establishing genomic
prediction models and line selection in the breeding program.
• Successfully deployed and tested GOBii instance for SBDM-
NARS partners
• MABC cases in sorghum using FlapJack
• Genomic prediction in chickpea, closely linked with ICAR
chickpea breeding programs (IARI, IIPR, AICRP)
• Genomic prediction in sorghum, closely linked with ICAR
sorghum breeding programs (IIMR, AICRP, SAUs)
Visualization tools and use cases

9. Kelly Robbins/ Liz Jones
Director
Monica
Fransiscus
Administrator
Liz Jones
Project
Manager
Yaw Nti-
Addae
Lead
Developer
Josh Lamos-
Sweeny
Software
Developer
Phil Glaser
UI Developer
Kevin Palis
DB Developer
Raza Syed
DB Developer
Angel Villahoz-
Baleta
Scientific
Programmer
Star Gao
Breeding
Informatics
Dave
Mathews
Consultant
• Susan McCouch
• Ed Buckler
• Jean-Luc Jannink
• Lukas Mueller
• Mark Sorrels
• Qi Sun
• Mike Olsen
• Susanne Dresigacker
• Rajeev K. Varshney
• Tobias Kretzschmar
• R. Mauleon
Principle Investigators
• M. Roorkiwal
• H. Kudapa
• A. Rathore
• R. Das
• V. Anil Kumar
• P. Bajaj
• S. Sivasubramani
• S. Chaitanya
• S. Deshpande
• P. Gaur/ H Gandhi
• S Srinivasan
• A. Kumar/ M Govindaraj
• P. Modi
ICRISAT
• J. C. Ignacio
• V. M. Juanillas
• J. Detras
• A. M. Raquel
• V. Calaminos
• N. Alexandrov
• M. Krakkainen
• M. Van den Berg
• Josh Cobb
• G. Kotch
IRRI
• V. J. Ulat
• K. Dreher
• X. Zhang
• R. Shrestha
• C. Ayada
• J. Riis-Jacobsen
• S. J. Hearne
• U. Rosyara
CIMMYT
SAB
• Steve Rounsley
• Julie Ho
• Nirav Merchant
• Rebecca Doerge
• Amy L Williams
• Dorian Garrick
• Jan Erik Backlund
• Dan Stanzione
• Dean Podlich

10. Thank you!