Large-scale transcriptome characterization and mass discovery of SNPs in globe artichoke and its related taxa

Davide Scaglione, Sergio Lanteri, Alberto Acquadro, Zhao Lai, Steven J. Knapp, Loren Rieseberg, Ezio Portis

Research output: Contribution to journalArticle

29 Scopus citations

Abstract

Cynara cardunculus (2n=2×=34) is a member of the Asteraceae family that contributes significantly to the agricultural economy of the Mediterranean basin. The species includes two cultivated varieties, globe artichoke and cardoon, which are grown mainly for food. Cynara cardunculus is an orphan crop species whose genome/transcriptome has been relatively unexplored, especially in comparison to other Asteraceae crops. Hence, there is a significant need to improve its genomic resources through the identification of novel genes and sequence-based markers, to design new breeding schemes aimed at increasing quality and crop productivity. We report the outcome of cDNA sequencing and assembly for eleven accessions of C. cardunculus. Sequencing of three mapping parental genotypes using Roche 454-Titanium technology generated 1.7×106 reads, which were assembled into 38726 reference transcripts covering 32Mbp. Putative enzyme-encoding genes were annotated using the KEGG-database. Transcription factors and candidate resistance genes were surveyed as well. Paired-end sequencing was done for cDNA libraries of eight other representative C. cardunculus accessions on an Illumina Genome Analyzer IIx, generating 46×106 reads. Alignment of the IGA and 454 reads to reference transcripts led to the identification of 195400 SNPs with a Bayesian probability exceeding 95%; a validation rate of 90% was obtained by Sanger-sequencing of a subset of contigs. These results demonstrate that the integration of data from different NGS platforms enables large-scale transcriptome characterization, along with massive SNP discovery. This information will contribute to the dissection of key agricultural traits in C. cardunculus and facilitate the implementation of marker-assisted selection programs.

Original languageEnglish (US)
Pages (from-to)956-969
Number of pages14
JournalPlant Biotechnology Journal
Volume10
Issue number8
DOIs
StatePublished - Oct 2012
Externally publishedYes

Keywords

  • Cynara cardunculus
  • Next generation sequencing
  • SNP
  • Transcriptome
  • de novo assembly

ASJC Scopus subject areas

  • Biotechnology
  • Agronomy and Crop Science
  • Plant Science

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