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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

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Free PMC article

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

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

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.

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.

Figures

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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