Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant Solanum melongena with interest for breedingReport as inadecuate

Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant Solanum melongena with interest for breeding - Download this document for free, or read online. Document in PDF available to download.

BMC Genomics

, 17:300

Plant genomics


BackgroundSolanum incanum is a close wild relative of S. melongena with high contents of bioactive phenolics and drought tolerance. S. aethiopicum is a cultivated African eggplant cross-compatible with S. melongena. Despite their great interest in S. melongena breeding programs, the genomic resources for these species are scarce.

ResultsRNA-Seq was performed with NGS from pooled RNA of young leaf, floral bud and young fruit tissues, generating more than one hundred millions raw reads per species. The transcriptomes were assembled in 83,905 unigenes for S. incanum and in 87,084 unigenes for S. aethiopicum with an average length of 696 and 722 bp, respectively. The unigenes were structurally and functionally annotated based on comparison with public databases by using bioinformatic tools. The single nucleotide variant calling analysis SNPs and INDELs was performed by mapping our S. incanum and S. aethiopicum reads, as well as reads from S. melongena and S. torvum available on NCBI database National Center for Biotechnology Information, against the eggplant genome. Both intraspecific and interspecific polymorphisms were identified and subsets of molecular markers were created for all species combinations. 36 SNVs were selected for validation in the S. incanum and S. aethiopicum accessions and 96 % were correctly amplified confirming the polymorphisms. In addition, 976 and 1,278 SSRs were identified in S. incanum and S. aethiopicum transcriptomes respectively, and a set of them were validated.

ConclusionsThis work provides a broad insight into gene sequences and allelic variation in S. incanum and S. aethiopicum. This work is a first step toward better understanding of target genes involved in metabolic pathways relevant for eggplant breeding. The molecular markers detected in this study could be used across all the eggplant genepool, which is of interest for breeding programs as well as to perform marker-trait association and QTL analysis studies.

KeywordsSolanum incanum S. aethiopicum Eggplant genepool De novo transcriptome Gene annotation Molecular marker discovery AbbreviationsEC numberenzyme commission number

ESTsExpressed sequence tag

FISHfluorescence in situ hybridization

GATKgenome analysis tool kit

GO termgene ontology term

HRMhigh resolution melting


KEGGkyoto encyclopedia of genes and genomes

NCBInational center for biotechnology information

ncRNAsnoncoding RNAs

NGSnext-generation sequencing

NR databasenon-redundant protein database

ORFopen reading frame

SNPsingle nucleotide polymorphism

SNVssingle nucleotide variations

SSRsimple sequence repeat

UTRuntranslated region

VCFvariant call format

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-016-2631-4 contains supplementary material, which is available to authorized users.

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Author: P. Gramazio - J. Blanca - P. Ziarsolo - F. J. Herraiz - M. Plazas - J. Prohens - S. Vilanova



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