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

0473313 - ÚEB 2017 RIV US eng J - Článek v odborném periodiku
Stočes, Štěpán - Ruttink, T. - Bartoš, Jan - Studer, B. - Yates, S. - Zwierzykowski, Z. - Abrouk, Michael - Roldán-Ruiz, I. - Książczyk, T. - Rey, Elodie - Doležel, Jaroslav - Kopecký, David
Orthology Guided Transcriptome Assembly of Italian Ryegrass and Meadow Fescue for Single-Nucleotide Polymorphism Discovery.
Plant Genome. Roč. 9, č. 3 (2016). E-ISSN 1940-3372
Grant CEP: GA ČR GAP501/11/05043; GA MŠMT(CZ) LO1204
Institucionální podpora: RVO:61389030
Klíčová slova: festuca-pratensis huds. * dna-sequencing data * lolium-perenne l. * rna-seq data * genome * cultivars * festulolium * multiflorum * hybrid * recombination
Kód oboru RIV: EB - Genetika a molekulární biologie
Impakt faktor: 2.736, rok: 2016

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.
Trvalý link: http://hdl.handle.net/11104/0270462