Abstract
In contrast to small genome model species where whole genome “shotgun sequencing” is sufficient, physical maps are mandatory for the development of whole genome reference sequences of large and complex genomes, such as those of the Triticeae crop species wheat, barley, and rye. Access to a whole genome physical map allows efficient and nearly unlimited isolation of genes that underpin biological mechanisms and agronomical traits. The basic methodologies (fingerprinting, assembly) for constructing such maps were established years ago and are applicable generally to any kind of genome. However, the size and features of the wheat and barley genomes require specific considerations when developing the most cost efficient strategy.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Ashida T, Nasuda S, Sato K, et al. (2007) Dissection of barley chromosome 5 H in common wheat. Genes Genet Syst 82: 123–133
Aston C, Mishra B, Schwartz D C (1999) Optical mapping and its potential for large-scale sequencing projects. Trends Biotechnol 17: 297–302
Bennett M D, Smith J B (1976) Nuclear DNA amounts in angiosperms. Philos Trans R Soc Lond B Biol Sci 274: 227–274
Bilgic H, Cho S, Garvin D F et al. (2007) Mapping barley genes to chromosome arms by transcript profiling of wheat–barley ditelosomic chromosome addition lines. Genome 50: 898–906
Burke D T, Carle G F, Olson M V (1987) Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 236: 806–812
Cheng C H, Chung M C, Liu S M, et al. (2005) A fine physical map of the rice chromosome 5. Mol Genet Genom 274: 337–345
Cheng Z, Buell C, Wing R, et al. (2002) Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers. Chromosome Res 10: 379–387
Cho S, Garvin D F, Muehlbauer G J (2006) Transcriptome analysis and physical mapping of barley genes in wheat-barley chromosome addition lines. Genetics 172: 1277–1285
Coulson A, Sulston J, Brenner S, et al. (1986) Toward a physical map of the genome of the nematode Caenorhabditis elegans. Proc Natl Acad Sci USA 83: 7821–7825
Cox D R (1992) Radiation hybrid mapping. Cytogenet Cell Genet 59: 80–81
Dean F B, Hosono S, Fang L, et al. (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci 99: 5261–5266
Dear P H, Cook P R (1989) HAPPY mapping: A proposal for linkage mapping the human genome. Nucleic Acids Res 17: 6795–6807
Dimalanta E T, Lim A, Runnheim R, et al. (2004) A microfluidic system for large DNA molecule arrays. Anal Chem 76: 5293–5301
Ding Y, Johnson M D, Chen W Q et al. (2001) Five-color-based high-information-content fingerprinting of bacterial artificial chromosome clones using type IIS restriction endonucleases. Genomics 74: 142–154
Ding Y, Johnson M D, Colayco R, et al. (1999) Contig assembly of bacterial artificial chromosome clones through multiplexed fluorescence-labeled fingerprinting. Genomics 56: 237–246
Doležel J, Kubaláková M, Bartoš J, et al. (2005) Chromosome flow sorting and physical mapping. In: Meksem K, Kahl G (eds.), The handbook of plant genome mapping. Genetic and physical mapping. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, 151–171
Doležel J, Kubaláková M, Paux E, et al. (2007) Chromosome-based genomics in the cereals. Chromosome Res 15: 51–66
Endo T (2007) The gametocidal chromosome as a tool for chromosome manipulation in wheat. Chromosome Res 15: 67–75
Endo T R (1988) Induction of chromosomal structural changes by a chromosome of Aegilops cylindrica L. In common wheat. J Hered 79: 366–370
Endo T R, Gill B S (1996) The deletion stocks of common wheat. J Hered 87: 295–307
Feuillet C, Eversole K (2008) Physical mapping of the wheat genome: A coordinated effort to lay the foundation for genome sequencing and develop tools for breeders. Isr J Plant Sci 55: 307–313
Flavell R B, Bennett M D, Smith J B, et al. (1974) Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem Genet 12: 257–269
Gill K S (2004) Gene distribution in cereal genomes. In: Gupta PK, Varshney RK (eds.), Cereal genomics. Kluwer Academic Publishers, Dordrecht, Boston, London, pp 361–384
Goss S J, Harris H (1975) New method for mapping genes in human chromosomes. Nature 255: 680–684
Hitte C, Madeoy J, Kirkness E F, et al. (2005) Facilitating genome navigation: Survey sequencing and dense radiation-hybrid gene mapping. Nat Rev Genet 6: 643–648
Jander G, Norris S R, Rounsley S D, et al. (2002) Arabidopsis map-based cloning in the post-genome era. Plant Physiol 129: 440–450
Jiang J, Gill B S (1994) Nonisotopic in situ hybridization and plant genome mapping: The first 10 years. Genome 37: 717–725
Jiang J, Gill B S (2006) Current status and the future of fluorescence in situ hybridization (fish) in plant genome research. Genome 49: 1057–1068
Jing J, Reed J, Huang J, et al. (1998) Automated high resolution optical mapping using arrayed, fluid-fixed DNA molecules. Proc Natl Acad Sci USA 95: 8046–8051
Joppa L (1993) Chromosome engineering in tetraploid wheat. Crop Sci 33: 908–913
Joppa L, Williams N (1988) Langdon durum disomic substitution lines and aneuploid analysis in tetraploid wheat. Genome 30: 222–228
Kalavacharla V, Hossain K, Gu Y, et al. (2006) High-resolution radiation hybrid map of wheat chromosome 1D. Genetics 173: 1089–1099
Kuenzel G, Korzun L, Meister A (2000) Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154: 397–412
Kynast R G, Okagaki R J, Galatowitsch M W, et al. (2004) Dissecting the maize genome by using chromosome addition and radiation hybrid lines. Proc Natl Acad Sci USA 101: 9921–9926
Lage J M, Leamon J H, Pejovic T, et al. (2003) Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-cgh. Genome Res. 13: 294–307
Lander E S, Waterman M S (1988) Genomic mapping by fingerprinting random clones: A mathematical analysis. Genomics 2: 231–239
Lapitan N L V, Brown S E, Kennard W, et al. (1997) Fish physical mapping with barley BAC clones. Plant J 11: 149–156
Leyser O, Chang C (1996) Chromosome walking. In: Foster GD, Twell D (eds.), Plant gene isolation. John Wiley and Sons, Ltd, Chichester, pp 248–271
Luo M-C, Thomas C, You F M, et al. (2003a) High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82: 378–389
Luo M C, Thomas C S, Deal K R, et al. (2003b) Construction of contigs of Aegilops tauschii genomic DNA fragments cloned in BAC and BIBAC vectors. In: 10th International Wheat genetics Symposium, September 1–6, 2003, Paestum, Italy, pp 293–296
Madishetty K, Condamine P, Svensson J T, et al. (2007) An improved method to identify bac clones using pooled overgos. Nucleic Acids Res 35: e5
Marra M A, Kucaba T A, Dietrich N L, et al. (1997) High throughput fingerprint analysis of large-insert clones. Genome Res 7: 1072–1084
Masoudi-Nejad A, Nasuda S, Bihoreau M-T, et al. (2005) An alternative to radiation hybrid mapping for large-scale genome analysis in barley. Mol Genet Genom 274: 589–594
Meksem K, Ishihara H, Jesse T (2005) Integration of physical and genetic maps. In: Meksem K, Kahl G (eds.), The handbook of plant genome mapping. Genetic and physical mapping. WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim, 215–232
Meyers B C, Scalabrin S, Morgante M (2004) Mapping and sequencing complex genomes: Let’s get physical! Nat Rev Genet 5: 578–588
Nasuda S, Kikkawa Y, Ashida T, et al. (2005) Chromosomal assignment and deletion mapping of barley est markers. Genes Genet Syst 80: 357–366
Olson M V, Dutchik J E, Graham M Y et al. (1986) Random-clone strategy for genomic restriction mapping in yeast. Proc Natl Acad Sci USA 83: 7826–7830
Paux E, Roger D, Badaeva E, et al. (2006) Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through bac-end sequencing on chromosome 3b. Plant J 48: 463–474
Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P, Korol A, Michalak M, Kianian S, Spielmeyer W et al. (2008) A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B. Science 322: 101–104
Pedersen C, Linde-Laursen I (1995) The relationship between physical and genetic distances at the hor1 and hor2 loci of barley estimated by two-colour fluorescent in situ hybridization. Theor Appl Genet 91: 941–946
Peters J L, Cnudde F, Gerats T (2003) Forward genetics and map-based cloning approaches. Trends Plant Sci 8: 484–491
Qi L, Echalier B, Friebe B, et al. (2003) Molecular characterization of a set of wheat deletion stocks for use in chromosome bin mapping of ESTs. Funct. Integr. Genomics 3: 39–55
Qi L L, Echalier B, Chao S, et al. (2004) A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 168: 701–712
Rayburn A, Biradar D, Bullock D, et al. (1993) Nuclear DNA content in F1 hybrids of maize. Heredity 70: 294–300
Ren C, Xu Z, Sun S, et al. (2005) Genomic DNA libraries and physical mapping. In: Meksem K, Kahl G (eds.), The handbook of plant genome mapping. Genetic and physical mapping. WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim, 173–214
Riera-Lizarazu O, Vales M I, Ananiev E V et al. (2000) Production and characterization of maize chromosome 9 radiation hybrids derived from an oat-maize addition line. Genetics 156: 327–339
Sadder M T, Weber G (2002) Comparison between genetic and physical maps in Zea mays L. of molecular markers linked to resistance against Diatreae spp. Theor Appl Genet 104: 908–915
Safar J, Bartos J, Janda J, et al. (2004) Dissecting large and complex genomes: Flow sorting and BAC cloning of individual chromosomes from bread wheat. Plant J 39: 960–968
Schwartz D C, Li X, Hernandez L, I et al. (1993) Ordered restriction maps of saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 262: 110–114
Shi F, Endo T (1997) Production of wheat-barley disomic addition lines possessing an aegilops cylindrica gametocidal chromosome. Genes Genet Syst 72: 243–248
Shizuya H, Birren B, Kim U-J, et al. (1992) Cloning and stable maintenance of 300-kilobase fragments of human DNA in Escherichia coli using and f-factor-based vector. Proc Natl Acad Sci USA 89: 8794–8797
Soderlund C, Humphray S, Dunham, A et al. (2000) Contigs built with fingerprints, markers, and FPC v4.7. Genome Res 10: 1772–1787
Soderlund C, Longden I, Mott R (1997) FPC: A system for building contigs from restriction fingerprinted clones. Comp Appl Biosci 13: 523–535
Stein N, Graner A (2004) Map-based gene isolation in cereal genomes. In: Gupta P, Varshney R (eds.), Cereal genomics. Kluwer Academic Publishers, Dordrecht, The Netherlands, pp 331–360
Stephens J L, Brown S E, Lapitan N L V, et al. (2004) Physical mapping of barley genes using an ultrasensitive fluorescence in situ hybridization technique. Genome 47: 179–189
Sulston J, Mallett F, Durbin R, et al. (1989) Image analysis of restriction enzyme fingerprint autoradiograms. Comp Appl Biosci 5: 101–106
Sulston J, Mallett F, Staden R, et al. (1988) Software for genome mapping by fingerprinting techniques. Comp Appl Biosci 4: 125–132
Telenius H, Carter N P, Bebb C E, et al. (1992) Degenerate oligonucleotide-primed pcr: General amplification of target DNA by a single degenerate primer. Genomics 13: 718–725
Thangavelu M, James A B, Bankier A, et al. (2003) HAPPY mapping in a plant genome: Reconstruction and analysis of a high-resolution physical map of a 1.9 Mbp region of Arabidopsis thaliana chromosome 4. Plant Biotech J 1: 23–31
The International Human Genome Mapping C (2001) A physical map of the human genome. Nature 409: 934–941
Valarik M, Bartos J, Kovarova P, et al. (2004) High-resolution FISH on super-stretched flow-sorted plant chromosomes. Plant J 37: 940–950
Varshney R K, Grosse I, Haehnel U et al. (2006) Genetic mapping and bac assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome. Theor Appl Genet 113: 239–250
Wang C-J R, Harper L, Cande W Z (2006) High-resolution single-copy gene fluorescence in situ hybridization and its use in the construction of a cytogenetic map of maize chromosome 9. Plant Cell 18: 529–544
Wardrop J, Fuller J, Powell W, et al. (2004) Exploiting plant somatic radiation hybrids for physical mapping of expressed sequence tags. Theor Appl Genet 108: 343–348
Wardrop J, Snape J, Powell W, et al. (2002) Constructing plant radiation hybrid panels. Plant J 31: 223–228
Waugh R, Dear P H, Powell W et al. (2002) Physical education – new technologies for mapping plant genomes. Trends Plant Sci 7: 521–523
Wei F, Coe E, Nelson W, et al. (2007) Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet 3: e123
Wendl M C, Waterston R H (2002) Generalized gap model for bacterial artificial chromosome clone fingerprint mapping and shotgun sequencing. Genome Res 12: 1943–1949
Wong G K S, Yu J, Thayer E C et al. (1997) Multiple-complete-digest restriction fragment mapping: Generating sequence-ready maps for large-scale DNA sequencing. Proc Natl Acad Sci USA 94: 5225–5230
Wu C, Sun S, Lee M-K, et al. (2005) Whole-genome physical mapping: An overview on methods for DNA fingerprinting. In: Meksem K, Kahl G (eds.), The handbook of plant genome mapping. Genetic and physical mapping. WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim, pp 257–306
You F M, Luo M-C, Gu Y Q, et al. (2007) Genoprofiler: Batch processing of high-throughput capillary fingerprinting data. Bioinformatics 23: 240–242
Yu Y, Tomkins J P, Waugh R, et al. (2000) A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes. Theor Appl Genet 101: 1093–1099
Zhang L, Cui X, Schmitt K, et al. (1992) Whole genome amplification from a single cell: Implications for genetic analysis. Proc Natl Acad Sci 89: 5847–5851
Zhou S, Bechner M C, Place M, et al. (2007) Validation of rice genome sequence by optical mapping. BMC Genomics 8: 278
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Stein, N. (2009). Physical Mapping in the Triticeae. In: Muehlbauer, G., Feuillet, C. (eds) Genetics and Genomics of the Triticeae. Plant Genetics and Genomics: Crops and Models, vol 7. Springer, New York, NY. https://doi.org/10.1007/978-0-387-77489-3_11
Download citation
DOI: https://doi.org/10.1007/978-0-387-77489-3_11
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-0-387-77488-6
Online ISBN: 978-0-387-77489-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)