Single nucleotide polymorphism discovery in elite north American potato germplasm

John P. Hamilton, Candice N. Hansey, Brett R. Whitty, Kevin Stoffel, Alicia N. Massa, Allen Van Deynze, Walter S. De Jong, David S. Douches, C. Robin Buell

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198 Scopus citations

Abstract

Background: Current breeding approaches in potato rely almost entirely on phenotypic evaluations; molecular markers, with the exception of a few linked to disease resistance traits, are not widely used. Large-scale sequence datasets generated primarily through Sanger Expressed Sequence Tag projects are available from a limited number of potato cultivars and access to next generation sequencing technologies permits rapid generation of sequence data for additional cultivars. When coupled with the advent of high throughput genotyping methods, an opportunity now exists for potato breeders to incorporate considerably more genotypic data into their decision-making.Results: To identify a large number of Single Nucleotide Polymorphisms (SNPs) in elite potato germplasm, we sequenced normalized cDNA prepared from three commercial potato cultivars: 'Atlantic', 'Premier Russet' and 'Snowden'. For each cultivar, we generated 2 Gb of sequence which was assembled into a representative transcriptome of ~28-29 Mb for each cultivar. Using the Maq SNP filter that filters read depth, density, and quality, 575,340 SNPs were identified within these three cultivars. In parallel, 2,358 SNPs were identified within existing Sanger sequences for three additional cultivars, 'Bintje', 'Kennebec', and 'Shepody'. Using a stringent set of filters in conjunction with the potato reference genome, we identified 69,011 high confidence SNPs from these six cultivars for use in genotyping with the Infinium platform. Ninety-six of these SNPs were used with a BeadXpress assay to assess allelic diversity in a germplasm panel of 248 lines; 82 of the SNPs proved sufficiently informative for subsequent analyses. Within diverse North American germplasm, the chip processing market class was most distinct, clearly separated from all other market classes. The round white and russet market classes both include fresh market and processing cultivars. Nevertheless, the russet and round white market classes are more distant from each other than processing are from fresh market types within these two groups.Conclusions: The genotype data generated in this study, albeit limited in number, has revealed distinct relationships among the market classes of potato. The SNPs identified in this study will enable high-throughput genotyping of germplasm and populations, which in turn will enable more efficient marker-assisted breeding efforts in potato.

Original languageEnglish (US)
Article number302
JournalBMC Genomics
Volume12
DOIs
StatePublished - Jun 9 2011

Bibliographical note

Funding Information:
We thank David Francis, Lukas Mueller, and Alex Stone for contributions to the SolCAP project. Funding for this project was provided by grants to D.D, D.F., A.V D., W. D, L.M., A.S. and C. R. B. by the U.S. Department of Agriculture National Institute of Food and Agriculture (2008-55300-04757 and 2009-85606-05673). We acknowledge the provision of the DM genome sequence by the Potato Genome Sequencing Consortium.

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