Solanaceae Genomics Resource

Spud DB is a collection of datasets and data-mining tools to view and analyze the potato genome, including tools to facilitate breeding improved cultivars.

Potato Genomic Tools

Potato (Solanum tuberosum L.) is the fourth most important crop in the world, behind wheat, rice, and maize. In 2004, worldwide potato production exceeded 327 million metric tons. Potato also produces more food energy and value per unit of land area than any other crop. Compared to grain crops, potato is a superior source of nutrition; however, among major crop plants, potato is arguably the most intensively managed. In addition, tuber quality requirements are complex and must be maintained during harvest and storage. The genome sequence of potato was released and published in 2011 by the International Potato Genome Sequencing Consortium (PGSC). The assembled potato genome is that of the doubled monoploid S. tuberosum Group Phureja DM1-3 (DM; AEWC00000000); the genome assembly represents 726 MB, of which 86%, is anchored to the genetic map and contains 39,031 annotated genes. In addition, BAC and whole genome shotgun sequences were released from a second clone, S. tuberosum Group Tuberosum RH89-039-16 (RH; ERP000627).

Spud DB houses potato genome browsers for the newly released version PGSC v4.03 pseudomolecules and for the previous PGSC v2.1.11 pseudomolecule release. The browsers contain information for the PGSC and the International Tomato Annnotation Group (ITAG) loci, hits to Arabidopsis, grape, poplar, tomato, and PlantGDB transcript assemblies for 12 other Solanaceae species. The potato genome browsers also contain data from 56 RNA-Seq libraries from DM (SRA030516) and RH (ERP000527), and SolCAP SNP information (Hamilton et al. 2011) (Felcher et al. 2012).

Each transcript annotated by the PGSC and the ITAG groups has a transcript report page that displays transcript and predicted protein sequences along with matches to UniRef, InterPro, Arabidopsis, tomato, and other potato sequences. Information is also available for SSRs, SNPs, and expression (FPKM) values in 56 tissues for the sequence.

Potato Breeding Tools

Through the SolCAP project, resources focused on translating genomic advances in potato to US breeding programs. We developed 'Breeder's Assistant' tools to provide easy and quick access to potato genotypic and phenotypic data. The tools currently focus on the SolCAP potato 8303 SNP Infinium array (Hamilton et al. 2011) (Felcher et al. 2012) and the data generated by a 250 clone diversity panel (Hirsch et al. 2013)

We welcome input from outside researchers. If there is some way in which we can improve this resource, we would like to hear from you. Please use the comment form on our contact page to send us your suggestions.

Funding has been provided by awards from the U.S. Department of Agriculture (2008-35300-18671) and the U.S. National Science Foundation (DBI-0604907, DBI-0834044, and 1202724). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Spud DB is maintained and hosted by the Buell Lab in the Plant Biology Department at Michigan State University.

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What's New

November 20, 2019

The haplotype resolved genome assembly and annotation of the heterozygous diploid potato RH89-039-16 is now avaiaible on SpudDB. More information about the assembly, download links, and a Jbrowse instance are available on the data access page..

February 5, 2018

The paper Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity been published in The Plant Journal. The genome assembly and annotation are available from the Data Dryad data repository.

February 1, 2016

The Buell Lab has released v4.04 of the DM pseudomolecules. More information can be found on the Download page

June 19, 2015

SNPs for the Solanum tuberosum cultivars Atlantic and Superior are now available as tracks on the Spud DB genome browser

September 8, 2014

The BLAST tool has been updated and now uses NCBI BLAST instead of the previous WU-BLAST. The output from the BLAST search now includes a graphical summary and an enhanced output layout as well.

April 4, 2014

An update has been made to the Breeder's Assistant Tools. Searching for SNPs via gene annotation is no longer case sensitive, leading to more complete search results.

March 28, 2014

A paper describing the resources, tools and data available in Spud DB has been published in the journal The Plant Genome.

Maintenance Notice

We have planned server maintenance on the first Wednesday of every month and therefore, Spud DB web pages may be unavailable or only partially functional during server maintenance.