capfitogen tools. facilitated spatial and ecogeographical germplasm analysis for efficient pgr...
DESCRIPTION
Presentation from the conference ENHANCED GENEPOOL UTILIZATION ‒ Capturing wild relative and landrace diversity for crop improvement, June 2014, Cambridge, UKTRANSCRIPT
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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)
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Funded by:
And with technical support of:
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Development
Transfer
Training
Building Capacity
National Programs and institutions
from Latin America
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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 ecogeographicapproaches on PGR
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40° 20’ 33.4’’ N03° 11’ 52.1’’ W
Or paper maps…Gazeteers…Georeferencing softwareOld records…
Evaluate the quality of your collecting sites coordinates and locality description
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Quality assessment on the georeferencing of the collecting sites included in passport data
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Based on: Parra-Quijano et al., 2012. Gen Res Crop Evol59(2):205-217
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Obtaining Ecogeographic Land Characterization (ELC) maps for a single species or group of related (specific maps) or unrelated species (generalist maps)
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Ecogeographic germplasm (collecting sites) characterizations
Up to 105 ecogeographicvariables
EcogeographicCharacterizationmatrix
GeoreferencedPassport data
GIS
Elevation
Annual mean temp
Organic carbon on soil
pH soil
….….
Y
X
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Perform ecogeographic characterizations of the georeferenced collecting sites
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• Is your collection representative of the species’ environmental adaptive range?
Check the ecogeographical representativeness of your ex situ collection
GAPS!REPRESENTED
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Evaluation of the ecogeographicalrepresentativeness of the germplasm collections
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• 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 studyAndean regionEcuador
Inspired onVan Zonneveld et al., 2012. PLoS ONE 7(1): e29845
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Obtaining phenotipic, genotypic or ecogeographic“diversity” maps
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Select a subset of accessions which represents the species’ ecogeographical range in your collection
A B
A
A
A
A
B
B B
B
C BA
A
B C
AA
AAB
B
BB
CBA
C
AA
A
A
AA
AA
CAB
A
B
CEcogeographicCoreCollection
Based on Parra Quijano et al., 2011. Crop Science 51:656-666
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Generation of ecogeographic core collections based on ELC maps
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Creating subsets of accessions with high probability to contain interesting traits
Annualprecipitation
Clay content
Slope
40
4
10% selectionintensity
FIGS subset (by filtering method)
Based on FIGS approach by Mackay,M., Street, K., Bari, A., Endresen, D. and other researchers
Waterlogging tolerance
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Generation of subsets of breeding interest traits based on ecogeographic conditions of the collecting sites (Focused Identification Germplasm Strategy – filtering method)
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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
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GEOQUAL +
ELCmapas +
Representa +
FIGS_R
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Spanish
Portuguese
English
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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
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Programme to Strengthen
National Plant Genetic
Resource Capacities in Latin
America
Phase 1:
2012-2014
Seven tools focused on ex situ conservationUser guidesThree languages (Spanish, English, Portuguese)Two regional (Latin American) workshopsFour national workshops (Cuba, Spain, Honduras, Uruguay)About 150 trained technicians
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Programme to Strengthen
National Plant Genetic
Resource Capacities in Latin
America
Phase 2:
2014-2016
Three new tools focused on in situ conservationUser’s networksE-Learning methodsTools on server (internet connection required, no installation)One final regional (Latin America + Spain + Portugal) workshopFour national workshops
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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
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http://www.agrobiodiversidad.org/blog/?p=1039
http://www.planttreaty.org/capfitogen