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A gap analysis methodology for collecting crop genepools: a case study with phaseolus beans.

Ramírez-Villegas J, Khoury C, Jarvis A, Debouck DG, Guarino L - PLoS ONE (2010)

Bottom Line: The methodology prioritizes among taxa based on a combination of sampling, geographic, and environmental gaps.We apply the gap analysis methodology to wild taxa of the Phaseolus genepool.Results of the gap analysis method mostly align very well with expert opinion of gaps in ex situ collections, with only a few exceptions.

View Article: PubMed Central - PubMed

Affiliation: Decision and Policy Analysis Program, International Center for Tropical Agriculture, Cali, Colombia. j.r.villegas@cgiar.org

ABSTRACT

Background: The wild relatives of crops represent a major source of valuable traits for crop improvement. These resources are threatened by habitat destruction, land use changes, and other factors, requiring their urgent collection and long-term availability for research and breeding from ex situ collections. We propose a method to identify gaps in ex situ collections (i.e. gap analysis) of crop wild relatives as a means to guide efficient and effective collecting activities.

Methodology/principal findings: The methodology prioritizes among taxa based on a combination of sampling, geographic, and environmental gaps. We apply the gap analysis methodology to wild taxa of the Phaseolus genepool. Of 85 taxa, 48 (56.5%) are assigned high priority for collecting due to lack of, or under-representation, in genebanks, 17 taxa are given medium priority for collecting, 15 low priority, and 5 species are assessed as adequately represented in ex situ collections. Gap "hotspots", representing priority target areas for collecting, are concentrated in central Mexico, although the narrow endemic nature of a suite of priority species adds a number of specific additional regions to spatial collecting priorities.

Conclusions/significance: Results of the gap analysis method mostly align very well with expert opinion of gaps in ex situ collections, with only a few exceptions. A more detailed prioritization of taxa and geographic areas for collection can be achieved by including in the analysis predictive threat factors, such as climate change or habitat destruction, or by adding additional prioritization filters, such as the degree of relatedness to cultivated species (i.e. ease of use in crop breeding). Furthermore, results for multiple crop genepools may be overlaid, which would allow a global analysis of gaps in ex situ collections of the world's plant genetic resources.

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Related in: MedlinePlus

Coverage of genebank accessions versus potential environmental area for modeled species for the first (left) and second (right) principal components.
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Related In: Results  -  Collection


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pone-0013497-g005: Coverage of genebank accessions versus potential environmental area for modeled species for the first (left) and second (right) principal components.

Mentions: P. vulgaris and P. lunatus showed the highest coverage of potential environmental range, with 8 and 14 respectively out of the 20 classes along PC1, and 8 and 16 classes along PC2 (Figure 5). Germplasm representativeness of these environmental classes is for both species significantly high (90% or more representativeness in both classes). For wild P. vulgaris, among other cases (Figure 5), we found the environmental distribution of genebank accessions to be broader than the environmental distribution of the potential distribution coverage, which may be explained as an artifact given the use of the ROC-plot based threshold for binning the species distributions (i.e. the omission rate), the native area (i.e. one or two small localities where the taxon occurs might not be reported in literature), or the use of the CA50 around germplasm locations, which might enlarge the range towards unsuitable habitats, particularly where the landscape changes rapidly (e.g. topographically diverse regions, such as the Andes). A broad range of adaptation to climatic conditions may be covered by current germplasm collections, but it should be noted that small environmental gaps remain even for these well-sampled species.


A gap analysis methodology for collecting crop genepools: a case study with phaseolus beans.

Ramírez-Villegas J, Khoury C, Jarvis A, Debouck DG, Guarino L - PLoS ONE (2010)

Coverage of genebank accessions versus potential environmental area for modeled species for the first (left) and second (right) principal components.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2958131&req=5

pone-0013497-g005: Coverage of genebank accessions versus potential environmental area for modeled species for the first (left) and second (right) principal components.
Mentions: P. vulgaris and P. lunatus showed the highest coverage of potential environmental range, with 8 and 14 respectively out of the 20 classes along PC1, and 8 and 16 classes along PC2 (Figure 5). Germplasm representativeness of these environmental classes is for both species significantly high (90% or more representativeness in both classes). For wild P. vulgaris, among other cases (Figure 5), we found the environmental distribution of genebank accessions to be broader than the environmental distribution of the potential distribution coverage, which may be explained as an artifact given the use of the ROC-plot based threshold for binning the species distributions (i.e. the omission rate), the native area (i.e. one or two small localities where the taxon occurs might not be reported in literature), or the use of the CA50 around germplasm locations, which might enlarge the range towards unsuitable habitats, particularly where the landscape changes rapidly (e.g. topographically diverse regions, such as the Andes). A broad range of adaptation to climatic conditions may be covered by current germplasm collections, but it should be noted that small environmental gaps remain even for these well-sampled species.

Bottom Line: The methodology prioritizes among taxa based on a combination of sampling, geographic, and environmental gaps.We apply the gap analysis methodology to wild taxa of the Phaseolus genepool.Results of the gap analysis method mostly align very well with expert opinion of gaps in ex situ collections, with only a few exceptions.

View Article: PubMed Central - PubMed

Affiliation: Decision and Policy Analysis Program, International Center for Tropical Agriculture, Cali, Colombia. j.r.villegas@cgiar.org

ABSTRACT

Background: The wild relatives of crops represent a major source of valuable traits for crop improvement. These resources are threatened by habitat destruction, land use changes, and other factors, requiring their urgent collection and long-term availability for research and breeding from ex situ collections. We propose a method to identify gaps in ex situ collections (i.e. gap analysis) of crop wild relatives as a means to guide efficient and effective collecting activities.

Methodology/principal findings: The methodology prioritizes among taxa based on a combination of sampling, geographic, and environmental gaps. We apply the gap analysis methodology to wild taxa of the Phaseolus genepool. Of 85 taxa, 48 (56.5%) are assigned high priority for collecting due to lack of, or under-representation, in genebanks, 17 taxa are given medium priority for collecting, 15 low priority, and 5 species are assessed as adequately represented in ex situ collections. Gap "hotspots", representing priority target areas for collecting, are concentrated in central Mexico, although the narrow endemic nature of a suite of priority species adds a number of specific additional regions to spatial collecting priorities.

Conclusions/significance: Results of the gap analysis method mostly align very well with expert opinion of gaps in ex situ collections, with only a few exceptions. A more detailed prioritization of taxa and geographic areas for collection can be achieved by including in the analysis predictive threat factors, such as climate change or habitat destruction, or by adding additional prioritization filters, such as the degree of relatedness to cultivated species (i.e. ease of use in crop breeding). Furthermore, results for multiple crop genepools may be overlaid, which would allow a global analysis of gaps in ex situ collections of the world's plant genetic resources.

Show MeSH
Related in: MedlinePlus