title: Identification of SNP and SSR markers in eggplant using RAD tag sequencing.
abstract: BACKGROUND
  The eggplant (Solanum melongena L.) genome is relatively unexplored, especially compared to those of the other major Solanaceae crops tomato and potato. In particular, no SNP markers are publicly available; on the other hand, over 1,000 SSR markers were developed and publicly available. We have combined the recently developed Restriction-site Associated DNA (RAD) approach with Illumina DNA sequencing for rapid and mass discovery of both SNP and SSR markers for eggplant.
  
  
  RESULTS
  RAD tags were generated from the genomic DNA of a pair of eggplant mapping parents, and sequenced to produce ~17.5 Mb of sequences arrangeable into ~78,000 contigs. The resulting non-redundant genomic sequence dataset consisted of ~45,000 sequences, of which ~29% were putative coding sequences and ~70% were in common between the mapping parents. The shared sequences allowed the discovery of ~10,000 SNPs and nearly 1,000 indels, equivalent to a SNP frequency of 0.8 per Kb and an indel frequency of 0.07 per Kb. Over 2,000 of the SNPs are likely to be mappable via the Illumina GoldenGate assay. A subset of 384 SNPs was used to successfully fingerprint a panel of eggplant germplasm, producing a set of informative diversity data. The RAD sequences also included nearly 2,000 putative SSRs, and primer pairs were designed to amplify 1,155 loci.
  
  
  CONCLUSIONS
  The high throughput sequencing of the RAD tags allowed the discovery of a large number of DNA markers, which will prove useful for extending our current knowledge of the genome organization of eggplant, for assisting in marker-aided selection and for carrying out comparative genomic analyses within the Solanaceae family.
authors.affiliation: DIVAPRA Plant Genetics and Breeding, University of Torino, Grugliasco, Italy.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Barchi
authors.forename: Sergio
authors.initials: S
authors.lastname: Lanteri
authors.forename: Ezio
authors.initials: E
authors.lastname: Portis
authors.forename: Alberto
authors.initials: A
authors.lastname: Acquadro
authors.forename: Giampiero
authors.initials: G
authors.lastname: Valè
authors.forename: Laura
authors.initials: L
authors.lastname: Toppino
authors.forename: Giuseppe Leonardo
authors.initials: GL
authors.lastname: Rotino
mesh_terms: D001665:Binding Sites; D002874:Chromosome Mapping; D004262:DNA Restriction Enzymes / Q000378:metabolism*; D018744:DNA, Plant / Q000235:genetics* / Q000378:metabolism*; D023281:Genomics; D018598:Minisatellite Repeats / Q000235:genetics*; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D032323:Solanum melongena / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D004262:DNA Restriction Enzymes