Skip to main content
ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Publications at this Location » Publication #306764

Title: Assessing SNPs versus RAPDs for predicting heterogeneity and screening efficiency in wild potato (Solanum)species

Author
item Bamberg, John
item DEL RIO, A - University Of Wisconsin
item COOMBS, J - Michigan State University
item DOUCHES, D - Michigan State University

Submitted to: American Journal of Potato Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/21/2014
Publication Date: 4/1/2015
Publication URL: http://handle.nal.usda.gov/10113/60743
Citation: Bamberg, J., del Rio, A., Coombs, J., Douches, D. 2015. Assessing SNPs versus RAPDs for predicting heterogeneity and screening efficiency in wild potato (Solanum) species. American Journal of Potato Research. 92(2):276-283.

Interpretive Summary: The potato crop has a large and rich pool of related germplasm for breeding in the US Potato Genebank. With so much material to screen it would be a great help if DNA markers could be used to predict the patterns of genetic variation within populations and species. We used SNPs, a new technique that is faster and gives more data than previous DNA markers to look at 8 populations of each of 4 model wild potato species. This study confirmed that these species are all very rich in genetic diversity. However, there are also clear differences in how that diversity is partitioned. For two of the species, the DNA markers predict that most traits could be isolated easily by screening bulks of populations. For the other two species, the DNA markers predict that one needs to look at individual plants within populations to isolate and detect the trait of interest. These differences in species are key for devising strategies for most efficiently prospecting for traits in the species, maximizing preservation of the genetic diversity in the genebank, and maximizing the collection of genes from the wild.

Technical Abstract: Knowing how genetic diversity is partitioned among and within wild potato species populations is important for efficient sampling for collection, preservation and evaluation. We sought to evaluate the effectiveness of SNPs for assessing germplasm by using the exact set of four model species previously evaluated by RAPDs. To avoid large numbers of SNP samples, population bulks of 25 plants were used, and original RAPD data was adjusted to match SNP genotype data. It was noted that especially for SNPs, it was necessary to examine only loci polymorphic within species to get a realistic view of genetic partitioning within species. This resulted in only a few hundred useful loci for some species. When considering among-population versus within-population partitioning of diversity, both SNPs and RAPDs usually distinguished the species as expected according to their known breeding system. Primitive wild species were confirmed as very heterogeneous. For most species, SNPs generated on replicate samples varied by < 1%. Both SNP and RAPD markers can be used to help breeders and genebank managers understand patterns in potato germplasm diversity.