Orthology Guided Transcriptome Assembly of Italian Ryegrass and Meadow Fescue for Single-Ncleotide Polymorphism Discovery

Stepan Stoces, Tom Ruttink, Jan Bartos, Bruno Studer, Steven Yates, Zbigniew Zwierzykowski, Michael Abrouk, Isabel Roldan-Ruiz, Tomasz Ksiazczyk, Elodie Rey, Jaroslav Dolezel, David Kopecky

    Onderzoeksoutput: Bijdrage aan tijdschriftA1: Web of Science-artikel

    Uittreksel

    Single-nucleotide polymorphisms (SNPs) represent natural DNA sequence variation. They can be used for various applications including the construction of high-density genetic maps, analysis of genetic variability, genome-wide association studies, and mapbased cloning. Here we report on transcriptome sequencing in the two forage grasses, meadow fescue (Festuca pratensis Huds.)
    and Italian ryegrass (Lolium multiflorum Lam.), and identification of various classes of SNPs. Using the Orthology Guided Assembly (OGA) strategy, we assembled and annotated a total of 18,952 and 19,036 transcripts for Italian ryegrass and meadow fescue, respectively. In addition, we used transcriptome sequence data of perennial ryegrass (L. perenne L.) from a previous study to
    identify 16,613 transcripts shared across all three species. Large numbers of intraspecific SNPs were identified in all three species: 248,000 in meadow fescue, 715,000 in Italian ryegrass, and 529,000 in perennial ryegrass. Moreover, we identified almost 25,000 interspecific SNPs located in 5343 genes that can distinguish meadow fescue from Italian ryegrass and 15,000 SNPs
    located in 3976 genes that discriminate meadow fescue from both Lolium species. All identified SNPs were positioned in silico on the seven linkage groups (LGs) of L. perenne using the GenomeZipper approach. With the identification and positioning of interspecific SNPs, our study provides a valuable resource for the grass research and breeding community and will enable detailed characterization of genomic composition and gene expression analysis in prospective Festuca x Lolium hybrids.
    TaalEngels
    TijdschriftPlant Genome
    Volume9
    Exemplaarnummer3
    Pagina's (van-tot)1-14
    ISSN1940-3372
    DOI's
    StatusGepubliceerd - 2016

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