CAPFITOGEN tools. Facilitated spatial and ecogeographical germplasm analysis for efficient PGR conservation and utilization

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Presentation from the conference ENHANCED GENEPOOL UTILIZATION ‒ Capturing wild relative and landrace diversity for crop improvement, June 2014, Cambridge, UK

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CAPFITOGEN tools. Facilitated spatial and ecogeographical germplasm analysis for efficient PGR conservation and utilization

  1. 1. Tools Facilitated spatial and ecogeographical germplasm analysis for efficient PGR conservation and utilization Mauricio Parra Quijano (ITPGRFA - Programme Coordinator) Francisco López (ITPGRFA) Elena Torres (UPM-Spain) José Iriondo (URJC-Spain)
  2. 2.  
  3. 3. Funded by: And with technical support of:
  4. 4. Development Transfer Training Building Capacity National Programs and institutions from Latin America
  5. 5. Idea + methodology development Theoretical and practical scientific validation Publication (peer review) Data preparation R script development Java / tomcat interface Tool + documentation Assistance CAPFITOGEN tool release / distribution GIS and ecogeographic approaches on PGR
  6. 6. 40° 20’ 33.4’’ N 03° 11’ 52.1’’ W Or paper maps… Gazeteers… Georeferencing software Old records… Evaluate the quality of your collecting sites coordinates and locality description
  7. 7. Quality assessment on the georeferencing of the collecting sites included in passport data
  8. 8. Based on: Parra-Quijano et al., 2012. Gen Res Crop Evol 59(2):205-217
  9. 9. Obtaining Ecogeographic Land Characterization (ELC) maps for a single species or group of related (specific maps) or unrelated species (generalist maps)
  10. 10. Ecogeographic germplasm (collecting sites) characterizations Up to 105 ecogeographic variables Ecogeographic Characterization matrix Georeferenced Passport data GIS Elevation Annual mean temp Organic carbon on soil pH soil …. …. Y X
  11. 11. Perform ecogeographic characterizations of the georeferenced collecting sites
  12. 12. • Is your collection representative of the species’ environmental adaptive range? Check the ecogeographical representativeness of your ex situ collection GAPS! REPRESENTED
  13. 13. Evaluation of the ecogeographical representativeness of the germplasm collections
  14. 14. • Ocurrence of the highest levels of diversity in terms of average genotypic, phenotypic or ecogeographic distances among local Identify where is located the diversity hotspots using phenotypic, genotypic or ecogeographic data Maize study Andean region Ecuador Inspired on Van Zonneveld et al., 2012. PLoS ONE 7(1): e29845
  15. 15. Obtaining phenotipic, genotypic or ecogeographic “diversity” maps
  16. 16. Select a subset of accessions which represents the species’ ecogeographical range in your collection A B A A A A B BB B C BA A B C A A A AB B B B CBA C A A A A A A A A CAB A B CEcogeographic Core Collection Based on Parra Quijano et al., 2011. Crop Science 51:656-666
  17. 17. Generation of ecogeographic core collections based on ELC maps
  18. 18. Creating subsets of accessions with high probability to contain interesting traits Annual precipitation Clay content Slope 40 4 10% selection intensity FIGS subset (by filtering method) Based on FIGS approach by Mackay,M., Street, K., Bari, A., Endresen, D. and other researchers Waterlogging tolerance
  19. 19. Generation of subsets of breeding interest traits based on ecogeographic conditions of the collecting sites (Focused Identification Germplasm Strategy – filtering method)
  20. 20. CAPFITOGEN tools offer: • Avoiding collecting in sites where other have been collecting in past expeditions • Collecting germplasm in under or non-represented environments • Collecting germplasm in sites with high probably of traits of interest occurrence
  21. 21. GEOQUAL + ELCmapas + Representa + FIGS_R
  22. 22. Spanish Portuguese English
  23. 23.  105 ecogeographical variables to select  With data available for more than 160 countries (national work frames)  Two sub-continental work frames (South and Meso- America)  One continent (Europe) and a world-wide work frame  1x1, 5x5, 10x10 and 20x20 km resolutions  Free access, free distribution
  24. 24. Programme to Strengthen National Plant Genetic Resource Capacities in Latin America Phase 1: 2012-2014 Seven tools focused on ex situ conservation User guides Three languages (Spanish, English, Portuguese) Two regional (Latin American) workshops Four national workshops (Cuba, Spain, Honduras, Uruguay) About 150 trained technicians
  25. 25. Programme to Strengthen National Plant Genetic Resource Capacities in Latin America Phase 2: 2014-2016 Three new tools focused on in situ conservation User’s networks E-Learning methods Tools on server (internet connection required, no installation) One final regional (Latin America + Spain + Portugal) workshop Four national workshops
  26. 26. Madrid, Spain, Nov 2013 Bogotá, Colombia, March 2013 Colonia, Uruguay, April 2014 Comayagua, Honduras, Nov 2013 Sancti Spitirus, Cuba, Sept 2013 Florianópolis, Brazil, May 2014 Birmingham, UK, Feb 2014
  27. 27. http://www.agrobiodiversidad.org/blog/?p=1039 http://www.planttreaty.org/capfitogen capfitogen@fao.org Mauricio.parra@fao.org Email:

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