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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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Validation results.(A) Frequency distribution of the relative difference [RD] and (B) linear trend between Final Priority Score (FPS) and Expert Priority Score (EPS) (the red dotted line indicates a 95% confidence interval).
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pone-0013497-g007: Validation results.(A) Frequency distribution of the relative difference [RD] and (B) linear trend between Final Priority Score (FPS) and Expert Priority Score (EPS) (the red dotted line indicates a 95% confidence interval).

Mentions: In comparison to expert opinion, the gap analysis approach tended to underestimate priority for collecting in a considerable number of cases (30.9% of the taxa); however, scores for 28 taxa (34.6%) did align with expert opinion (with 0 as score for 24 of these). For 51 taxa (63%), the method and DGD agreed on the priority class, and from the remaining proportion, the difference was of one single class. In addition, the relative difference (RD) varied from −50% to 72.2% and the maximum difference between our approach and the expert's concept was around 7 units in the priority scale of 10 units. Moreover, 87.7% of the validated taxa (81) presented differences lower than 30% or greater than −30%, and only 2 taxa presented more than a 50% or less than −50% difference (P. salicifolius with 7.2 in EPS and 0 in FPS, P. marechalii with 8.3 in EPS and 3 in FPS). Only P. salicifolius was found to have more than 70% difference between EPS and FPS (Figure 7a).


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)

Validation results.(A) Frequency distribution of the relative difference [RD] and (B) linear trend between Final Priority Score (FPS) and Expert Priority Score (EPS) (the red dotted line indicates a 95% confidence interval).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0013497-g007: Validation results.(A) Frequency distribution of the relative difference [RD] and (B) linear trend between Final Priority Score (FPS) and Expert Priority Score (EPS) (the red dotted line indicates a 95% confidence interval).
Mentions: In comparison to expert opinion, the gap analysis approach tended to underestimate priority for collecting in a considerable number of cases (30.9% of the taxa); however, scores for 28 taxa (34.6%) did align with expert opinion (with 0 as score for 24 of these). For 51 taxa (63%), the method and DGD agreed on the priority class, and from the remaining proportion, the difference was of one single class. In addition, the relative difference (RD) varied from −50% to 72.2% and the maximum difference between our approach and the expert's concept was around 7 units in the priority scale of 10 units. Moreover, 87.7% of the validated taxa (81) presented differences lower than 30% or greater than −30%, and only 2 taxa presented more than a 50% or less than −50% difference (P. salicifolius with 7.2 in EPS and 0 in FPS, P. marechalii with 8.3 in EPS and 3 in FPS). Only P. salicifolius was found to have more than 70% difference between EPS and FPS (Figure 7a).

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