Selection and validation of an AFLP marker core collection for the wild potato Solanum microdontum

Authors: Bamberg, John; DEL RIO, ALFONSO - University Of Wisconsin

Submitted to: American Journal of Potato Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/13/2013
Publication Date: 12/20/2013
Publication URL: http://handle.nal.usda.gov/10113/59402
Citation: Bamberg, J.B., del Rio, A. 2013. Selection and validation of an AFLP marker core collection for the wild potato Solanum microdontum. American Journal of Potato Research. 91(4):368-375.

Interpretive Summary: Exotic germplasm from the US Potato Genebank has made great contributions to the potato crop, and continues to have great potential. Its use in breeding is limited, in part, by the daunting scope and cost of evaluating so much germplasm. Thus, composition of smaller representative sets of germplasm could be very valuable. We here provide a case study in which a core set of S. microdontum populations was selected to capture the maximum number of DNA markers. A core of 59 (about 2/3 of all the populations available) included all the markers, provided balanced representation of the entire natural range of the species, both previous subspecies designations, and all three the genetic clusters. More importantly, it included populations with the best or almost best evaluation value for all of 26 previously-studied phenotypic traits. This retrospective success does not guarantee that the core will be equally likely to encompass new phenotypic traits, but it is encouraging. We expect that DNA marker-based core sets would have similar value if applied to other potato species.

Technical Abstract: Solanum microdontum is a diploid potato species with features that make it a good model for research into management and use of germplasm in the genebank. Its taxonomic status is unambiguous and it is in the taxonomic series of wild species closest to cultivated forms. It is represented by about 100 populations in the genebank—not too many for comprehensive evaluation, yet not too few to make prioritization of the most valuable populations worthwhile. This species is also particularly rich in desirable traits, often exhibiting very broad segregation. We here report use of DNA markers for selection of a core set of populations, and assessing whether that core captures populations with the most desirable evaluation results for economic traits. DNA was extracted from bulks of 27 plants from each of 94 populations to generate AFLPs. A total of 1741 informative loci were detected. AFLP loci were treated as though they were traits, with the banded condition considered to be the desired state to include in a core set. At least one band unique to a population was present in 45 populations, and these 45 populations together captured 98% of all bands. Adding another 14 populations for a core of 59 populations captured 100% of bands. This core set was assessed for whether it encompassed those populations known to have useful traits, including nutritional and quality components; and disease, stress and pest resistances. As with AFLP bands, 25 of 26 of the most desirable phenotypic traits were also found in populations in the core set of 59 populations. The most desirable status of 3 traits is lost by selecting a core of 45 populations. We conclude that these core sets would be a rational starting point when prospecting for new useful traits in microdontum.