Examples and applied use

An ex situ gap analysis was carried out for 73 of the closest wild relatives of potato (Solanum section Petota), including wild potatoes in the primary and secondary gene pools as well as any distant relatives in the thirtiary gene pool that have confimed or potential uses in crop breeding. The aim of this analysis was to establish priorities for further collecting to fill important gaps in germplasm collections.

Germplasm data were obtained from repositories easy to access, namely: EURISCO, GRIN and CIP’s biomart portal. Other species occurrence data and additional germplasm accessions passport data were gathered from various online databases and via communications with data managers, including GBIF, CRIA, SINGER, CPNWH, the Atlas of Guatemalan Crop Wild Relatives (Azurdia et al. 2011), the PBI Solanum—a worldwide treatment, LAC biosafety, as well as from literature (e.g. Spooner et al. 2014), and herbaria (i.e. E, K, L, NY, MA, PH, RB and US). The occurrence data collated and used in this analysis are available here. Potential distribution models were obtained for each species using MaxEnt (Phillips et al. 2006) based on a set of 19 bioclimatic variables derived from the WorldClim database (Hijmans et al. 2005) at a resolution of 2.5 arc-minutes (approx. 5 km at the equator). Performance of models was assessed based on three criteria: (i) the 5-fold average Area Under the Test ROC Curve (ATAUC), (ii) the standard deviation of the ATAUC for the 5 different folds, and (iii) the proportion of potential distribution where the standard deviation is greater than 0.15 (ASD15). A suitable model had to meet the following conditions: ATAUC >0.7, STAUC <0.15 and ASD15 <10% (Ramírez-Villegas et al. 2010). For those species where a suitable model was not obtained (either due to lack of data or low performance of the ensemble model), a convex hull (polygon surrounding the outermost georeferenced points) was prepared.

The gap analysis methodology used was that of Maxted et al. (2008) and of Ramírez-Villegas et al. (2010). Three metrics were used to prioritize CWR for collecting: a Sampling Representativeness Score (SRS) (compared the number of germplasm accessions to the total number of samples and provided an overview of the sufficiency of accessions per species), a Geographic Representativeness Score (GRS) [compared the distribution models with the geographic distribution of existing germplasm accession collecting sites, which was estimated by creating circular buffers of 50 km (CA50) around each site where the accession was collected (Hijmans et al. 2001), and which assessed the geographic coverage of germplasm collections], an Ecosystem Representativeness Score (ERS) [compared the number of ecosystems currently represented in ex situ collections with the total number of ecosystems distributed within the distribution models of each taxon, using a world terrestrial ecoregions map (Olson et al. 2001)]. Equal weight was given to these three metrics and an average was calculated to obtain a Final Priority Score (FPS). Collecting priorities were then categorized as follows: high priority species (HPS) when FPS ≤3, or when ten or less accessions were recorded in germplasm collections; medium-priority species (MPS) when 3< FPS ≥5; low priority species (LPS) when 5< FPS ≥7.5; and ‘no further collecting of germplasm required’ (NFCR) when 7.5< FPS ≥10. The gap analysis was performed using R v2.15.1 (R Core Team 2014) and various packages (see the paper for more details).

Priority areas for collecting ex situ gaps identified above were prepared for each species by subtracting the existing germplasm CA50 buffers from the potential distribution models. For those species where a niche model was not produced, CA50 buffers were prepared around all presence records and germplasm CA50 buffers were subtracted from the CA50 buffers of all presence records. Collecting gap maps for all high priority species were then obtained using the ‘Zonal Statistics’ tool in ArcMap 10.1 which produced a species richness map of further collecting per country of occurrence.

A total of 32 species (43.8%) were assigned high priority for further collecting, most of them located in Peru, the geographic centre of diversity of potato wild relatives. A total of 20 and 18 species were assessed as medium and low priority for further collecting, respectively, and only three species were considered to be sufficiently represented.

Source: Castañeda-Álvarez et al. (2015)