An AFLP Marker Core Subset for the Cultivated Potato Species Solanum phureja ( Solanum tuberosum L. subsp. andigenum)

AFLP markers were used to build a core subset in 144 accessions of the United States Potato Genebank (USPG) ex situ collection of the species formerly known as Solanum phureja (now reclassified as Solanum tuberosum L. subsp. andigenum). A core subset aims to sample the minimum number possible of non-redundant germplasm units capturing the maximum diversity of the entire collection. Characterization and trait evaluation of a core subset is expected to be easier and more effective when compared to the entire germplasm collection. In this study 1534 polymorphic AFLP markers were generated and demonstrated to be useful to determine genetic relationships in the materials used. All the accessions were clearly discriminated from each other with genetic similarity levels ranging from 62 to 89%, and no duplicate germplasm samples were detected. To create the core subset, the presence of the AFLP marker was considered as the genetic trait to retain and the selection of accessions was determined by their rankings on the number of most markers added to the core. The results of this selection process revealed that the 9 top-ranked accessions of phureja, when combined, achieved the benchmark of capturing 85% of the markers detected in the complete collection. Further selection to increase the percentage of marker capture added 17 accessions with unique marker contributions which resulted in a final core subset of 26 accessions capturing 96% of the marker diversity. A Principal Component analysis determined that spatial distribution of diversity in the core was a proportional sampling of the entire diversity of the collection validating the selecting approach used. A review of the public database for valuable traits for the USPG phureja germplasm revealed that the core subset also included accessions with desirable pest/disease resistances and stress tolerances (in 25 out of the 30 traits reported in the database). The USPG expects this core subset would create opportunities for facilitating evaluation and research by using a reduced set of germplasm units with nearly all the diversity of the entire set.