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Research Program Genetic Gains (RPGG) Review Meeting 2021: Update on Global open breeding informatics initiative By Dr Rajeev K Varshney

  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!
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