Spud DB: A Resource for Mining Sequences, Genotypes, and Phenotypes to Accelerate Potato Breeding

Abstract

Potato is the world's third most important crop, and is becoming increasingly important in developing countries. Cultivated potato is a highly heterozygous tetraploid (2n = 4x = 48) and suffers from significant inbreeding depression when selfed. As potato can be vegetatively propagated, breeding has been based primarily on phenotypic selection in F1 populations. However, recent advances in genome sequencing and genotyping methods have resulted in the development of large genomic, genetic, and phenotypic datasets that will enable more efficient and rapid breeding approaches. We have developed Spud DB (http:// potato.plantbiology.msu.edu/) for the community to access the potato genome sequence and associated annotation datasets, along with phenotypic and genotypic data from a diversity panel of 250 potato clones. The Breeder's Assistant is a web tool to retrieve pertinent phenotypic and genotypic data in a userguided manner, and query polymorphic markers such as single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) to identify custom sets of markers for a gene or region of interest. To browse and query the potato genome, a genome browser with 94 tracks of genome annotation, sequence variants, and expression abundance has been deployed. Spud DB also provides a comprehensive search page to data mine the potato genome through tools that query sequence identifiers, functional annotation, gene ontology (GO), InterPro domains, and basic local alignment search tool (BLAST) databases. Collectively, this resource links potato genomic data with phenotypic and genotypic data from a large collection of potato lines for use by the potato community, especially breeders and geneticists.

Fibrin(ogen)olytic and antiplatelet activities of a subtilisin-like protease from Solanum tuberosum (StSBTc-3)

“…Platelets readily aggregate in response to a variety of endogenous signals and secrete various compounds that cause further aggregation; they can initiate thrombus formation and precipitate thromboembolism, leading to ischemic diseases [48,49]. Antiplatelet activity has been reported for several plant proteases and plant extracts [16,50,51].…”

Informational Resources on Potato Germplasm Collections

“…На сайте SpudDB (Hirsch et al, 2014) представлена ин формация о геномных данных по картофелю. Прежде всего, это браузер генома картофеля, визуализирующий структуру хромосом и генов, геномные вариации, лока лизацию маркеров и др.…”

Eleven <i>StOSMs</i> Genes in the Potato Genome Response to Water Deficiency

“…The sequence of the cloned StOSM-3B cDNA was retrieved in the PGSC_DM_v3.4_gene.fasta file from the Potato Genome Sequencing Consortium website (http://solanaceae.plantbiology.msu.edu) (Cory et al 2014). A total of eleven StOSM genes distributed among five chromosomes in the potato genome were identified from the PGSC database.…”

“…StOSM family under water stress 1.2.1 StOSM expression analysis by mined RNA-Seq data Among the RNA-Seq data of S. tuberosum genotype RH89-039-16 from the published potato genome (Xu et al 2011 andCory et al 2014), the only available RNA-Seq data under water stress is from the RH leaf. Therefore, the RNA-Seq data for certain RH organs, including leaf with and without water stress, stem, roots, stolon and mature tuber, were selected and compared with respect to the expression of the eleven StOSM genes.…”

“…The sequence of the cloned StOSM cDNA was compared against the NCBI files and the PGSC_DM_v3.4_gene.fasta files from the Potato Genome Sequencing Consortium (PGSC) website (http://potatogenomics.plantbiology.msu.edu) (Xu et al 2011 andCory et al 2014). Using the downloaded sequences for the StOSM and promoter from the PGSC database, two phylogenetic trees for the StOSM peptides and promoters were constructed using the neighbour-joining method in the MEGA 5.02 software package developed by (Saitou andNei1987 andTamura et al 2007 …”