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  1. http://singer.cgiar.org/ http://code.google.com/p/bioversity-singer/issues/list ICIs developer workshop, ICRISAT, 28 March-1stapril 2011

  2. ‘Establishing a Genetic Resource Support Service (GRSS) to the plant breeding community’ GCP project CIRAD ICRISAT Bioversity SGRP

  3. Background • The CORE sample collection set was developed before 2005 and is made up of 2000/3000 accessions • This set was further filtered between 2005 and 2008 in order to create a set of 200/300 accessions denoted as MINICORE sample collection • Then the GCP identified a set of Genetic Stock accessions and created a set denoted as CORE Reference Set • Lastly, a NUCLEUS was indentified (less than 50 accessions) which included the accession representing all the genetic subgroups • It was agreed that all four of these sets (per crop) must be shown on SINGER

  4. Genetic Resources Support Services

  5. Genetic Resources Support Services • 16 excel files received from the CIRAD consultant Sarah Katherine Mcgrath for: Chickpea, Sorghum, Musa, Wheat, Maize, Barley, Coconut, Bean, Cowpea, Foxtail Millet, Finger Millet, Groundnut, Lentil, Pearl Millet, Pigeon Pea and Rice. • The excel files included the list of accessions included in the Reference Set for each crop.

  6. List of reference sets • Chickpea and Sorghum the lists of accessions identified as pertaining to the Core and Minicore Collections were downloaded from the ICRISAT website. • Chickpea Core • http://www.icrisat.org/what-we-do/crops/ChickPea/Project1/Core/Start.htm • Chickpea Minicore • http://test1.icrisat.org/ChickPea/Minicore.htm • Sorghum Core: • http://test1.icrisat.org/sorghum/Project1/Core/Start.htm • Sorghum Minicore • http://test1.icrisat.org/sorghum/Project1/Sorghum_minicore.htm • For Musa Core • http://gcpcr.grinfo.net/index.php?app=datasets&inc=dataset_details&dataset_id=576

  7. Genetic Resources Support Services

  8. Musa Reference Sets and SSR results

  9. Collecting crop diversity: Accessing the original observation data captured during plant exploration missions

  10. Original observation data is essential • Identify duplicates between collections and gaps in diversity – value for genebank curators and collecting actions • Tracking original sample and country of origin in pedigrees – value for Breeders and Benefit Sharing for donor countries Rice REgister

  11. Original observation: a treasure for genebanks and breeders The collecting form contains the botanical classification along with localization details, environment, cultural practices, diseases and pest presence and symptoms and traditional uses • Genus and Species • Collecting Number • Site Information: Admin boundaries, Latitude, Longitude and Elevation • Collecting Source and Sample Status

  12. Scanning of field notebooks and related documents • Collectors recorded key sample information (passport data) and other observation data in field books and collecting forms

  13. http://www.central-repository.cgiar.org/ A public repository of full scanned documents • 23,120 pdf files • African yam, Bambara Groundnut, Barley, Beans, Cassava, Chickpea, Cowpea, Finger millet, Forages, Groundnut, Maize, Musa, Pear millet, Pigeonpea, Potato, Rice, Sorghum, Tree genetic resources, Wheat, Wild vigna, and Yam. • The  Agricultural Research Centre (ARC) of Lao People’s Democratic Republic through joint Lao-IRRI collecting missions • The International Rice Research Institute (IRRI)AfricaRice, • International Institute on Tropical Agriculture (IITA) • Bioversity International • Accessible through SINGER for each collecting mission, through Rice, • Cassava repositories at passport level

  14. IBPGR/IPGRI supported germplasm collecting missions • 550 germplasm collecting missions • 225,000 samples • 3,755 species from 137 countries • Samples sent to 550genebanks worldwide for safety duplication, conservation and potential distribution • CGIAR centers received directly or indirectly germplasm and organized various collecting missions for their mandate crops

  15. Identification and quality-checking in databases • Different publicly available genebank inventories are checked in order to track corresponding samples and complete missing passport data information

  16. Data extraction summary from IBPGR/IPGRI supported missions • To date, 132,027 passport data records from 440 collecting missions have been extracted and integrated into Bioversity’s renewed sample level database

  17. Improved passport data sets from genebank inventories 65,000 of the samples records (50% of total) already linked to genebank accessions in 56 institutes worldwide 80,000 samples, collected in 30,000 different sites, are georeferenced (62% of total) 90% of residual 50,000 germplasm samples have locality information => georeference

  18. Collected Sample level database • Collected sample database for Bioversity supported collecting missions • Searchable PDF-Repository online with all scanned documents CGIAR-wide • Various projects to address gap analysis and diversity analysis, like Genesys, encourage partners to perform same work and share the full text and data

  19. SINGER maintenance Team in Bioversity SINGER database &Web site Raj Sood KiranViparthi Milko Skofic Guilhem Sempere Luca Matteis Elizabeth Arnaud GRSS prototype Federico Mattei Jean Francois Rami Guilhem Sempere Luca Matteis Collecting mission database & repository Hannes Gaisberger Federico Mattei Massimo Buonaiuto Andrea De Pirro Valentina Barbiero Simone Mori Silvia Lambiase Imke Thormann

  20. SINGER Focal Points: Genebank Database managers • Marimagne TCHAMBA - Africa Rice Center • Max RUAS – Bioversity International • Angela HERNANDEZ-CIAT • Efren RODRIGUEZ –CIMMYT • Reinhard SIMON –CIP • Jan KONOPKA -ICARDA  • Calleb ORWA-ICRAF • ThimmaREDDY -ICRISAT  • Matija OBREZA-IITA • Alexandra Maria Jorge - ILRI • Grace CAPILIT -IRRI  • AVRDC

  21. THANK YOU FOR YOUR ATTENTION!