SNP discovery using Paired-End RAD-tag sequencing on pooled genomic DNA of Sisymbrium austriacum (Brassicaceae)

K. Vandepitte, O. Honnay, Joachim Mergeay, P. Breyne, I. Roldán-Ruiz, T. De Meyer

    Onderzoeksoutput: Bijdrage aan tijdschriftA1: Web of Science-artikel

    Uittreksel

    Single nucleotide polymorphisms SNPs are rapidly replacing anonymous markers in population genomic studies, but their use in non model organisms is hampered by the scarcity of cost-effective approaches to uncover genome-wide variation in a comprehensive subset of individuals. The screening of one or only a few individuals induces ascertainment bias. To discover SNPs for a population genomic study of the Pyrenean rocket (Sisymbrium austriacum subsp. chrysanthum), we undertook a pooled RAD-PE (Restriction site Associated DNA Paired-End sequencing) approach. RAD tags were generated from the PstI-digested pooled genomic DNA of 12 individuals sampled across the species distribution range and paired-end sequenced using Illumina technology to produce ~24.5 Mb of sequences, covering ~7% of the specie's genome. Sequences were assembled into ~76 000 contigs with a mean length of 323 bp (N50 = 357 bp, sequencing depth = 24x). In all, >15 000 SNPs were called, of which 47% were annotated in putative genic regions based on homology with the Arabidopsis thaliana genome. Gene ontology (GO) slim categorization demonstrated that the identified SNPs covered extant genic variation well. The validation of 300 SNPs on a larger set of individuals using a KASPar assay underpinned the utility of pooled RAD-PE as an inexpensive genome-wide SNP discovery technique (success rate: 87%). In addition to SNPs, we discovered >600 putative SSR markers.
    TaalEngels
    TijdschriftMolecular Ecology Resources
    Volume13
    Pagina's (van-tot)269-275
    Aantal pagina's7
    ISSN1471-827
    DOI's
    StatusGepubliceerd - 2013

    Thematische lijst

    • Soorten en biotopen

    EWI Biomedische wetenschappen

    • B001-algemene-biomedische-wetenschappen

    Technologisch

    • genetische technieken

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