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. 2011 Jun 10;12:304.
doi: 10.1186/1471-2164-12-304.

Identification of SNP and SSR Markers in Eggplant Using RAD Tag Sequencing

Free PMC article

Identification of SNP and SSR Markers in Eggplant Using RAD Tag Sequencing

Lorenzo Barchi et al. BMC Genomics. .
Free PMC article


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.

Conclusion: 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.


Figure 1
Figure 1
Sequencing and gene annotation pipeline for eggplant RAD tags.
Figure 2
Figure 2
GO term representation (%) of eggplant genomic sequences according to the three high level GO categories.
Figure 3
Figure 3
Transitions and transversions occurring within a set of > 10,000 eggplant SNPs.
Figure 4
Figure 4
Phylogeny of 23 Solanum melongena genotypes along with one accession of S. aethiopicum. Genotyping was based on allele calls at 343 SNP loci. In brackets: fruits shapes (L: long; O: oval; R: round) of eggplant genotypes and indication of the parental lines of the F2 mapping population [9]. Asterisks indicate the progenitors of the '305E40' parental line.

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