Abstract
Analyses of large genomes are hampered by high proportions of repetitive DNA, that make the assembly of short sequence reads difficult. This is also the case for meadow fescue (Festuca pratensis Huds.), one of predominant grass species in temperate and Northern regions with the genome size estimated at 1C = 3,175 Mbp. This species is known for its ability to survive under freezing conditions and it has been used widely in intergeneric hybridization with various ryegrass species to produce superior Festulolium cultivars. Here we describe attempts to dissect the meadow fescue’s genome into smaller fractions—individual chromosomes and groups of chromosomes. Following the methods of flow cytogenetics developed for legumes and cereals, we have developed a chromosome sorting protocol for grasses and currently we are able to sort F. pratensis chromosome 4 (the largest in the genome) and two groups of three chromosomes each: 2, 3, 7 and 1, 5, 6. As the first step we sequenced chromosome 4 by Illumina with 50x coverage and assembled low copy and genic regions. This facilitated detailed comparative analysis with sequenced genomes of rice, Brachypodium and sorghum and provided the first insight into the genome composition of this species. The possibility to purify chromosome 4 opens the way for a more efficient analysis of genetic loci on this chromosome that control important agronomic traits, such as freezing tolerance. Moreover, purified chromosomes are excellent templates for PCR screening as well as cytogenetic and physical mapping.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Alm V, Fang C, Busso CS, Devos KM, Vollan K, Grieg Z, Rognli OA (2003) A linkage map of meadow fescue (Festuca pratensis Huds.). Theor Appl Genet 108:25–40
Bartoš J, Paux E, Kofler R, Havránková M, Kopecký D, Suchánková P, Šafář J, Šimková H, Town CD, Lelley T, Feuillet C, Doležel J (2008) A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R. BMC Plant Biol 8:95
Bartoš J, Sandve SR, Kölliker R, Kopecký D, Christelová P, Stočes S, Østrem L, Larsen A, Kilian A, Rognli OA and Doležel J (2011) Genetic mapping of DArT markers in the Festuca-Lolium complex and their use in freezing tolerance association analysis. Theor Appl Genet 122:1133–1147
Doležel J, Bartoš J, Voglmayr H, Greilhuber J (2003) Nuclear DNA content and genome size of trout and human. Cytometry 51:127–128
Doležel J, Kubaláková M, Vrána J, Bartoš J (2004) Flow cytogenetics. In: Goodman RM (ed) Encyclopedia of plant and crop science, Marcel Dekker, Inc., New York, pp 460–463
Doležel J, Šimková H, Kubaláková M, Šafář J, Suchánková P, Číhalíková J, Bartoš J, Valárik M (2009) Chromosome Genomics in the Triticeae. In: Feuillet C, Muehlbauer GJ (eds) Genetics and genomics of the triticeae, plant genetics and genomics: crops and models 7. Springer, Heidelberg, pp 285–316
Donnison IS, O’Sullivan DM, Thomas A, Canter P, Moore B, Armstead I, Thomas H, Edwards KJ, King IP (2005) Construction of a Festuca pratensis BAC library for map-based cloning in festulolium substitution lines. Theor Appl Genet 110:846–851
Farrar K, Asp T, Lubberstedt T, Xu M, Thomas AM, Christiansen C, Humphreys MO, Donnison IS (2007) Construction of two Lolium perenne BAC libraries and identification of BACs containing candidate genes for disease resistance and forage quality. Mol Breeding 19:15–23
Kofler R, Bartoš J, Gong L, Stift G, Suchánková P, Šimková H, Berenyi M, Burg K, Doležel J, Lelley T (2008) Development of microsatellite markers specific for the short arm of rye (Secale cereale L.) chromosome 1. Theor Appl Genet 117:915–926
Kopecky D, Lukaszewski AJ, Gibeault V (2005) Reduction of ploidy level by androgenesis in intergeneric Lolium-Festuca hybrids for turf grass breeding. Crop Sci 45:274–281
Kopecký D, Loureiro J, Zwierzykowski Z, Ghesquiere M, Dolezel J (2006) Genome constitution and evolution in Lolium´Festuca hybrid cultivars (Festulolium). Theor Appl Genet 113:731–742
Kopecký D, Lukaszewski AJ, Doležel J (2008a) Meiotic behaviour of individual chromosomes of Festuca pratensis in tetraploid Lolium multiflorum. Chromosome Res 16:987–998
Kopecký D, Lukaszewski AJ, Doležel J (2008b) Cytogenetics of Festulolium (Festuca´Lolium hybrids). Cytogenet Genome Res 120:370–383
Kopecký D, Bartoš J, Lukaszewski AJ, Baird JH, Černoch V, Kölliker R, Rognli OA, Blois H, Caig V, Lübberstedt T, Studer B, Shaw P, Doležel J, Kilian A (2009) Development and mapping of DArT markers within the–Festuca—Lolium complex. BMC Genomics 10:473
Kopecký D, Havránková M, Loureiro J, Castro S, Lukaszewski AJ, Bartoš J, Kopecká J, Doležel J (2010) Physical distribution of homoeologous recombination in individual chromosomes of Lolium multiflorum/Festuca pratensis substitutions. Cytogenet Genome Res 129:162–172
Kubaláková M, Valárik M, Bartoš J, Vrána J, Číhalíková J, Molnár-Lang M, Doležel J (2003) Analysis and sorting of rye (Secale cereale L.) chromosomes using flow cytometry. Genome 46:893–905
Martienssen RA, Rabinowicz PD, O’Shaughnessy A, McCombie WR (2004) Sequencing the maize genome. Curr Opin in Plant Biol 7:102–107
Mayer KFX, Martis M, Hedley PE, Šimková H, Liu H, Morris JA, Steuernagel B, Taudien S, Roessner S, Gundlach H, Kubaláková M, Suchánková P, Murat F, Felder M, Nussbaumer T, Graner A, Salse J, Endo T, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsumoto T, Scholz U, Doležel J, Waugh R, Stein N (2011) Unlocking the Barley Genome by Chromosomal and Comparative Genomics. Plant Cell 23:1249–1263
Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P, Korol A, Michalak M, Kianian S, Spielmeyer W, Lagudah E, Somers D, Kilian A, Alaux M, Vautrin S, Berges H, Eversole K, Appels R, Šafář J, Šimková H, Doležel J, Bernard M, Feuillet C (2008) A physical map of the 1-gigabase bread wheat chromosome 3B. Sci 322:101–104
Peterson DG, Wessler SR, Paterson AH (2002) Efficient capture of unique sequences from eukaryotic genomes. Trends Genet 18:547–550
Rabinowicz PD, Schutz K, Dedhia N, Yordan C, Pernell LD, Stein L, McCombie WR, Martienssen RA (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nat Genet 23:305–308
Šafář J, Šimková H, Kubaláková M, Číhalíková J, Suchánková P, Bartoš J, Doležel J (2010) Development of chromosome-specific BAC resources for genomics of bread wheat. Cytogenet Genome Res 129:211–223
Šimková H, Šafář J, Suchánková P, Kovářová P, Bartoš J, Kubaláková M, Janda J, Číhalíková J, Mago R, Lelley T, Doležel J (2008) A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS). BMC Genomics 9:237
Suchánková P, Kubaláková M, Kovářová P, Bartoš J, Číhalíková J, Molnár-Lang M, Endo TR, Doležel J (2006) Dissection of the nuclear genome of barley by chromosome flow sorting. Theor Appl Genet 113:651–659
Valárik M, Bartoš J, Kovářová P, Kubaláková M, de Jong JH, Doležel J (2004) High-resolution FISH on super-stretched flow-sorted plant chromosomes. Plant J 37:940–950
Vrána J, Kubaláková M, Šimková H, Číhalíková J, Lysák MA, Doležel J (2000) Flow-sorting of mitotic chromosomes in common wheat (Triticum aestivum L.). Genetics 156:2033–2041
Wenzl P, Suchánková P, Carling J, Šimková H, Huttner E, Kubaláková M, Sourdille P, Paul E, Feuillet C, Kilian A, Doležel J (2010) Isolated chromosomes as a new and efficient source of DArT markers for the saturation of genetic maps. Theor Appl Genet 121:465–474
Wicker T, Mayer KFX, Gundlach H, Martis M, Steuernagel B, Scholz U, Šimková H, Kubaláková M, Choulet F, Taudien S, Platzer M, Feuillet C, Fahima T, Budak H, Doležel J, Keller B, Stein N (2011) Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell 23:1706–1718.
Zhou RN and Hu ZM (2007) The development of chromosome microdissection and microcloning technique and its applications in genomic research. Curr Genomics 8:67–72
Acknowledgements
Authors would like to thank Prof. Adam J. Lukaszewski for critical reading and valuable comments.This work has been supported by the Czech Science Foundation (grant award P501/11/0504) and by the Ministry of Education, Youth and Sports of the Czech Republic and the European Regional Development Fund (Operational Programme Research and Development for Innovations No. CZ.1.05/2.1.00/01.0007).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media Dordrecht
About this paper
Cite this paper
Kopecký, D. et al. (2013). Establishing Chromosome Genomics in Forage and Turf Grasses. In: Barth, S., Milbourne, D. (eds) Breeding strategies for sustainable forage and turf grass improvement. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-4555-1_13
Download citation
DOI: https://doi.org/10.1007/978-94-007-4555-1_13
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-007-4554-4
Online ISBN: 978-94-007-4555-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)