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The Plant Genome Abstract - Original Research

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


This article in TPG

  1. Vol. 9 No. 3
    unlockOPEN ACCESS
    Received: Feb 16, 2016
    Accepted: June 06, 2016
    Published: July 28, 2016

    * Corresponding author(s): kopecky@ueb.cas.cz
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  1. Štěpán Stočesa,
  2. Tom Ruttinkb,
  3. Jan Bartoša,
  4. Bruno Studerc,
  5. Steven Yatesc,
  6. Zbigniew Zwierzykowskid,
  7. Michael Abrouka,
  8. Isabel Roldán-Ruizb,
  9. Tomasz Książczykd,
  10. Elodie Reya,
  11. Jaroslav Doležela and
  12. David Kopecký *a
  1. a Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
    b Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit–Growth and Development, Caritasstraat 39, 9090 Melle, Belgium
    c Institute of Agricultural Sciences, Forage Crop Genetics, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
    d Dep. of Environmental Stress Biology, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60479 Poznań, Poland
Core Ideas:
  • Transcriptomes of F. pratensis and L. multiflorum were sequenced and assembled
  • We present a catalogue of SNPs for ancestry analysis and future breeding of grasses
  • We defined interspecific SNPs to study parental-genome specific gene expression in hybrids
  • We positioned SNPs on linkage groups for high-resolution genome constitution analysis


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 map-based 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 × Lolium hybrids.

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