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Pfeifer M, Martis M, Asp T, Mayer KF, Lübberstedt T, Byrne S, Frei U, Studer B. The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics. PLANT PHYSIOLOGY 2013; 161:571-82. [PMID: 23184232 PMCID: PMC3561004 DOI: 10.1104/pp.112.207282] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 11/20/2012] [Indexed: 05/18/2023]
Abstract
Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.
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Affiliation(s)
- Matthias Pfeifer
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany (M.P., M.M., K.F.X.M.); Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A., S.B.); Department of Agronomy, Iowa State University, Ames, Iowa 50011 (T.L., U.F.); and Institute of Agricultural Sciences, Forage Crop Genetics, Eidgenössisch Technische Hochschule Zurich, 8092 Zurich, Switzerland (B.S.)
| | - Mihaela Martis
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany (M.P., M.M., K.F.X.M.); Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A., S.B.); Department of Agronomy, Iowa State University, Ames, Iowa 50011 (T.L., U.F.); and Institute of Agricultural Sciences, Forage Crop Genetics, Eidgenössisch Technische Hochschule Zurich, 8092 Zurich, Switzerland (B.S.)
| | - Torben Asp
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany (M.P., M.M., K.F.X.M.); Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A., S.B.); Department of Agronomy, Iowa State University, Ames, Iowa 50011 (T.L., U.F.); and Institute of Agricultural Sciences, Forage Crop Genetics, Eidgenössisch Technische Hochschule Zurich, 8092 Zurich, Switzerland (B.S.)
| | - Klaus F.X. Mayer
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany (M.P., M.M., K.F.X.M.); Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A., S.B.); Department of Agronomy, Iowa State University, Ames, Iowa 50011 (T.L., U.F.); and Institute of Agricultural Sciences, Forage Crop Genetics, Eidgenössisch Technische Hochschule Zurich, 8092 Zurich, Switzerland (B.S.)
| | - Thomas Lübberstedt
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany (M.P., M.M., K.F.X.M.); Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A., S.B.); Department of Agronomy, Iowa State University, Ames, Iowa 50011 (T.L., U.F.); and Institute of Agricultural Sciences, Forage Crop Genetics, Eidgenössisch Technische Hochschule Zurich, 8092 Zurich, Switzerland (B.S.)
| | - Stephen Byrne
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany (M.P., M.M., K.F.X.M.); Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A., S.B.); Department of Agronomy, Iowa State University, Ames, Iowa 50011 (T.L., U.F.); and Institute of Agricultural Sciences, Forage Crop Genetics, Eidgenössisch Technische Hochschule Zurich, 8092 Zurich, Switzerland (B.S.)
| | - Ursula Frei
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany (M.P., M.M., K.F.X.M.); Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A., S.B.); Department of Agronomy, Iowa State University, Ames, Iowa 50011 (T.L., U.F.); and Institute of Agricultural Sciences, Forage Crop Genetics, Eidgenössisch Technische Hochschule Zurich, 8092 Zurich, Switzerland (B.S.)
| | - Bruno Studer
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany (M.P., M.M., K.F.X.M.); Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A., S.B.); Department of Agronomy, Iowa State University, Ames, Iowa 50011 (T.L., U.F.); and Institute of Agricultural Sciences, Forage Crop Genetics, Eidgenössisch Technische Hochschule Zurich, 8092 Zurich, Switzerland (B.S.)
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Kopecký D, Bartoš J, Christelová P, Cernoch V, Kilian A, Doležel J. Genomic constitution of Festuca × Lolium hybrids revealed by the DArTFest array. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:355-63. [PMID: 20872131 DOI: 10.1007/s00122-010-1451-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 09/08/2010] [Indexed: 05/25/2023]
Abstract
Complementary attributes of Festuca and Lolium grasses can be combined in hybrid cultivars called Festuloliums, which are becoming increasingly popular fodder crops and amenity plants. Genomic constitution of commercially available Festuloliums was reported to vary from almost equal representation of parental genomes to apparent lack of one of them based on molecular cytogenetic analyses and screening with a small set of DNA markers, both approaches with limited resolution. Here, we describe the use of the DArTFest array comprising 3,884 polymorphic DArT markers for characterization of genomes in five Festulolium cultivars. In any of the cultivars, the minimum number of informative markers, which discriminated the parental Lolium and Festuca genomes was 361 and 171, respectively. Using the DArTFest array, it was possible to determine hybrid genome constitution at resolution which has never been achieved before and the analysis of a set of randomly selected plants from each cultivar provided information on genetic structure of outcrossing Festulolium cultivars. In addition to a core set of markers typical for each hybrid cultivar, markers occurring at low frequency among the plants within each cultivar were identified. Biological significance of genomic loci associated with the rare markers is yet to be determined. Finally, with the aim to simplify the use of DArTFest arrays to characterize Festuca × Lolium hybrids, various bulking strategies were compared. While all bulks were suitable for identification of hybrids, only bulks of few plants have been found to reveal the rare markers.
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Affiliation(s)
- David Kopecký
- Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovská 6, 77200, Olomouc, Czech Republic.
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