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Stočes Š, Ruttink T, Bartoš J, Studer B, Yates S, Zwierzykowski Z, Abrouk M, Roldán-Ruiz I, Książczyk T, Rey E, Doležel J, Kopecký D. Orthology Guided Transcriptome Assembly of Italian Ryegrass and Meadow Fescue for Single-Nucleotide Polymorphism Discovery. THE PLANT GENOME 2016; 9. [PMID: 27902806 DOI: 10.3835/plantgenome2016.02.0017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
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 ( Huds.) and Italian ryegrass ( 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.) 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 species. All identified SNPs were positioned in silico on the seven linkage groups (LGs) of 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 × hybrids.
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Dierking R, Azhaguvel P, Kallenbach R, Saha M, Bouton J, Chekhovskiy K, Kopecký D, Hopkins A. Linkage Maps of a Mediterranean × Continental Tall Fescue Population and their Comparative Analysis with Other Poaceae Species. THE PLANT GENOME 2015; 8:eplantgenome2014.07.0032. [PMID: 33228282 DOI: 10.3835/plantgenome2014.07.0032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 01/08/2015] [Indexed: 06/11/2023]
Abstract
Temperate grasses belonging to the Festuca-Lolium complex are important throughout the world in pasture and grassland agriculture. Tall fescue (Festuca arundinacea Schreb.) is the predominant species in the United States, covering approximately 15 million ha. Tall fescue has distinctive morphotypes, two of which are Continental (summer active) and Mediterranean (summer semidormant). This is the first report of a linkage map created for Mediterranean tall fescue, while updating the Continental map with additional simple sequence repeat and sequence-tagged site markers. Additionally, this is the first time that diversity arrays technology (DArT) markers were used in the construction of a tall fescue map. The male parent (Continental), R43-64, map consisted of 594 markers arranged in 22 linkage groups (LGs) and covered a total of 1577 cM. The female parent (Mediterranean), 103-2, map was shorter (1258 cM) and consisted of only 208 markers arranged in 29 LGs. Marker densities for R43-64 and 103-2 were 2.65 and 6.08 cM per marker, respectively. When compared with the other Poaceae species, meadow fescue (F. pratensis Huds.), annual ryegrass (L. multiflorum Lam.), perennial ryegrass (L. perenne L.), Brachypodium distachyon (L.) Beauv., and barley (Hordeum vulgare L.), a total of 171 and 98 orthologous or homologous sequences, identified by DArT analysis, were identified in R43-64 and 103-2, respectively. By using genomic in situ hybridization, we aimed to identify potential progenitors of both morphotypes. However, no clear conclusion on genomic constitution was reached. These maps will aid in the search for quantitative trait loci of various traits as well as help define and distinguish genetic differences between the two morphotypes.
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Affiliation(s)
- Ryan Dierking
- Dep. of Agronomy, Purdue Univ., 915 West State St., West Lafayette, IN, 47907
| | - Perumal Azhaguvel
- Syngenta, 2369- 330th Street, Slater, IA, 50244
- Forage Improvement Division, The Samuel Roberts Noble Foundation, Inc., Ardmore, OK
| | - Robert Kallenbach
- Division of Plant Sciences, Univ. of Missouri, 208 Waters Hall, Columbia, MO, 65211
| | - Malay Saha
- Forage Improvement Division, The Samuel Roberts Noble Foundation, Inc., Ardmore, OK
| | - Joseph Bouton
- Forage Improvement Division, The Samuel Roberts Noble Foundation, Inc., Ardmore, OK
| | | | - David Kopecký
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Slechtitelu 31,, Olomouc, 78371, Czech Republic
| | - Andrew Hopkins
- Dow AgroSciences, Inc., 1117 Recharge Rd., York, NE, 68467
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