The large bread wheat genome (1C ∼ 17 Gbp) contains a preponderance of repetitive DNA and the species is polyploid. These characteristics together serve to hamper the molecular analysis of the wheat genome. Its complexity can, however, be reduced by using flow cytometry to isolate individual chromosomes, and these can be exploited to construct chromosome-specific BAC libraries. Such libraries simplify the task of physical map construction, positional cloning and the targeted development of genetic markers. Rapid improvements in the efficiency and cost of DNA sequencing provide an opportunity to contemplate sequencing the wheat genome by preparing sequence-ready physical maps for each chromosome or chromosome arm in turn. The quality of the chromosome-specific libraries depends on their chromosome coverage and the mean insert size. First-generation libraries suffered from a relatively low mean insert size, but improvements to the protocol have generated a second wave of libraries with a significantly increased mean insert size and better chromosome coverage. Each chromosome (arm)-specific library is composed of a manageable number of clones, and so represents a practical tool in the area of wheat genomics.

Keywords:
BAC library, Chromosome, DNA markers, Flow sorting, Physical mapping, Wheat
1.
Akbari M, Wenzl P, Caig V, Carling J, Xia L, et al: Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet 113:1409–1420 (2006).
2.
Akhunov ED, Akhunova AR, Dvorak J: BAC libraries of Triticum urartu, Aegilops speltoides and Ae. tauschii, the diploid ancestors of plyploid wheat. Theor Appl Genet 111:1617–1622 (2005).
3.
Allouis S, Moore G, Bellec A, Sharp R, Faivre Rampant P, et al: Construction and characterisation of a hexaploid wheat (Triticum aestivum L.) BAC library from the reference germplasm Chinese Spring. Cereal Res Commun 31:331–338 (2003).
4.
Banks TW, Jorda MC, Somers DJ: Single-feature polymorphism mapping in bread wheat. Plant Gen 2:167–178 (2009).
5.
Bartoš J, Paux E, Kofler R, Havránková M, Kopecký D, et al: 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 (2008).
6.
Burke DT, Carle GF, Olson MV: Cloning of large fragments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 4803:806–812 (1987).
7.
Cenci A, Chantret N, Kong X, Gu Y, Anderson OD, et al: Construction and characterization of a half million clone BAC library of durum wheat (Triticum turgidum ssp. durum). Theor Appl Genet 107:931–939 (2003).
8.
Chalhoub B, Belcram H, Caboche M: Efficient cloning of plant genomes into bacterial artificial chromosome (BAC) libraries with larger and more uniform insert size. Plant Biotechnol J 2:181–188 (2004).
9.
Chantret N, Salse J, Sabot F, Rahman S, Bellec A, et al: Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell 17:1033–1045 (2005).
10.
Chen FG, Zhang XY, Xia GM, Jia JZ: Construction and characterization of a bacterial artificial chromosome library for Triticum boeoticum. Acta Botanica Sinica 44:451–456 (2002).
11.
Choulet F, Paux E, Salse J, Leroy P, Magdelenat G, et al: Sequencing, annotation and characterization of 17 Mb of chromosome 3B contigs provide novel insights into the wheat genome organization and evolution, in: Book of Abstracts, 19th International Triticeae Mapping Initiative and 3rd COST Tritigen, p 58, INRA, Clermont-Ferrand (2009).
12.
Chumakov I, Rigault P, Guillou S, Ougen P, Billaut A, et al: Continuum of overlapping clones spanning the entire human chromosome 21q. Nature 359:380–387 (1992).
13.
Coulson A, Sulston J, Brenner S, Karn J: Toward a physical map of the genome of the nematode Caenorhabditis elegans. Proc Natl Acad Sci USA 83:7821–7825 (1986).
14.
Devos KM, Doležel J, Feuillet C: Genome organization and comparative genomics, in Carver BF (ed): Wheat – Science and Trade, pp 327–367 (Wiley-Blackwell, Ames, Iowa 2009).
15.
Ding Y, Johnson MD, Chen WQ, Wong D, Chen YJ, et al: Five-color-based high-information-content fingerprinting of bacterial artificial chromosome clones using type IIS restriction endonucleases. Genomics 74:142–154 (2001).
16.
Doležel J, Číhalíková J, Lucretti S: A high-yield procedure for isolation of metaphase chromosomes from root tips of Vicia faba L. Planta 188:93–98 (1992).
17.
Doležel J, Kubaláková M, Bartoš J, Macas J: Flow cytogenetics and plant genome mapping. Chromosome Res 12:77–91 (2004).
18.
Doležel J, Kubaláková M, Paux E, Bartoš J, Feuillet C: Chromosome-based genomics in cereals. Chromosome Res 15:51–66 (2007).
19.
Endo TR, Gill BS: The deletion stocks of common wheat. J Hered 87:295–307 (1996).
20.
Feldman M, Levy AA: Allopolyploidy – a shaping force in the evolution of wheat genomes. Cytogenet Genome Res 109:250–258 (2005).
21.
Feuillet C, Travella S, Stein N, Albar L, Nublat A, Keller B: Map-based isolation of the leaf rust disease resistance gene Lr10 from the hexaploid wheat (Triticum aestivum L.) genome. Proc Natl Acad Sci USA 100:15253–15258 (2003).
22.
Gill BS, Li W, Sehgal SK, Faris J, Reddy L, et al: Progress towards the construction of a sequence-ready physical map of the 3AS chromosome arm of hexaploid wheat, in: Abstracts of the International Conference ‘Plant and Animal Genome XVI’, p 121(Sherago International, Inc., San Diego 2008).
23.
Gupta PK, Mir RR, Mohan A, Kumar J: Wheat genomics: present status and future prospects. Int J Plant Genomics 2008:1–37 (2008).
24.
Huang L, Brooks SA, Li WL, Fellers JP, Trick HN, Gill BS: Map-based cloning of leaf rust resistance gene Lr21 from the large and polyploid genome of bread wheat. Genetics 164:655–664 (2003).
25.
Ioannou PA, de Jong PJ: Construction of bacterial artificial chromosome libraries using the modified P1 (PAC) system. Current Protocols in Human Genetics, pp 5.15.1–5.15.24 (Wiley, New York 1996).
26.
Islam AKMR, Shepherd KW, Sparrow DHB: Isolation and characterization of euplasmic wheat-barley chromosome addition lines. Heredity 46:161–174 (1981).
27.
Janda J, Bartoš J, Šafář J, Kubaláková M, Valárik M, et al: Construction of a subgenomic BAC library specific for chromosomes 1D, 4D and 6D of hexaploid wheat. Theor Appl Genet 109:1337–1345 (2004).
28.
Janda J, Šafář J, Kubaláková M, Bartoš J, Kovář vá P, et al: Advanced resources for plant genomics: BAC library specific for the short arm of wheat chromosome 1B. Plant J 47:977–986 (2006).
29.
Kalavacharla V, Hossain K, Gu Y, Riera-Lizarazu O, Vales MI, et al: High-resolution radiation hybrid map of wheat chromosome 1D. Genetics 173:1089–1099 (2006).
30.
Kofler R, Bartoš J, Gong L, Stift G, Suchánková P, et al: Development of microsatellite markers specific for the short arm of rye (Secale cereale L.) chromosome 1. Theor Appl Genet 117:915–926 (2008).
31.
Krattinger S, Wicker T, Keller B: Map-based cloning of genes in Triticeae (wheat and barley), in Feuillet C, Muehlbauer GJ (eds): Genetics and Genomics of the Triticeae, pp 337–357 (Springer, Berlin 2009).
32.
Kubaláková M, Vrána J, Číhalíková J, Šimková H, Doležel J: Flow karyotyping and chromosome sorting in bread wheat (Triticum aestivum L.). Theor Appl Genet 104:1362–1372 (2002).
33.
Kubaláková M, Kovář vá P, Suchánková P, Číhalíková J, Bartoš J, et al: Chromosome sorting in tetraploid wheat and its potential for genome analysis. Genetics 170:823–829 (2005).
34.
Lijavetzky D, Muzzi G, Wicker T, Keller B, Wing R, Dubcovsky J: Construction and characterization of a bacterial artificial chromosome (BAC) library for the A genome of wheat. Genome 42:1176–1182 (1999).
35.
Ling P, Chen XM: Construction of a hexaploid wheat (Triticum aestivum L.) bacterial artificial chromosomelibrary for cloning genes for stripe rust resistance. Genome 48:1028–1036 (2005).
36.
Liu S, Pumphrey MO, Gill BS, Trick HN, Zhang JX, et al: Toward positional cloning of FHB1, a major QTL for Fusarium head blight resistance in wheat. Cereal Res Commun 36:195–201 (2008).
37.
Liu YG, Nagaki K, Fujita M, Kawaura K, Uozumi M, Ogihara Y: Development of an efficient maintenance and screening system for large-insert genomic DNA libraries of hexaploid wheat in a transformation-competent artificial chromosome (TAC) vector. Plant J 23:687–695 (2000).
38.
Luo MC, Thomas C, You FM, Hsiao J, Shu OY: High-throughput fingerprinting of bacterial artificial chromosomes using the SNaPshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82:378–389 (2003).
39.
Luo MC, Ma Y, Deal KR, Cao S, Šafář J, et al: Physical mapping of wheat genomes: Knowledge, resources and strategies, in: Abstracts of the International Conference ‘Plant and Animal Genome XVI’, p 67 (Sherago International, Inc., San Diego 2008).
40.
Luo MC, Xu K, Ma Y, Deal KR, Nicolet C, Dvorak J: A high-throughput strategy for screening of bacterial artificial chromosome libraries and anchoring of clones on a genetic map constructed with single nucleotide polymorphisms. BMC Genomics 10:28 (2009).
41.
Luo MC, Ma Y, You FM, Anderson OD, Kopecký D, et al.: Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species. BMC Genomics 11:122 (2010).
42.
Ma Z, Weining S, Sharp PJ, Liu C: Non-gridded library: a new approach for BAC (bacterial artificial chromosome) exploitation in hexaploid wheat (Triticum aestivum). Nucleic Acids Res 28:E106 (2000).
43.
Mardis ER: The impact of next-generation sequencing technology on genetics. Trends Genet 24:133–141 (2008).
44.
McNeil MD, Kota R, Paux E, Dunn D, McLean R, et al: BAC-derived markers for assaying the stem rust resistance gene, Sr2, in wheat breeding programs. Mol Breeding 22:15–24 (2008).
45.
Moullet O, Zhang HB, Lagudah ES: Construction and characterisation of a large DNA insert library from the D genome of wheat. Theor Appl Genet 99:305–313 (1999).
46.
Nilmalgoda SD, Cloutier S, Walichnowski AZ: Construction and characterization of a bacterial artificial chromosome (BAC) library of hexaploid wheat (Triticum aestivum L.) and validation of genome coverage using locus-specific primers. Genome 46:870–878 (2003).
47.
Ogihara Y, Mochida K, Kawaura K, Murai K, Seki M, et al: Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags. Genes Genet Syst 79:227–232 (2004).
48.
Paux E, Roger D, Badaeva E, Gay G, Bernard M, et al: Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J 48:463–474 (2006).
49.
Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, et al: A physical map of the 1-gigabase bread wheat chromosome 3B. Science 322:101–104 (2008).
50.
Perumal A, Weng Y, Ma Y, Luo MC, Šimková H, et al: A putative NBS-LRR candidate gene for aphid resistance in wheat, in: Abstracts of the International Conference ‘Plant and Animal Genomes XVIII’, p 296 (Sherago International, Inc., San Diego 2010).
51.
Peterson DG, Tomkins JP, Frisch DA, Wing RA, Paterson AH: Construction of plant bacterial artificial chromosome (BAC) libraries: An illustrated guide. J Agric Genom 5: http://www.ncgr.org/research/jag (2000).
52.
Pettersson E, Lundeberg J, Ahmadian A: Generations of sequencing technologies. Genomics 93:105–111 (2009).
53.
Ratnayaka I, Baga M, Fowler DB, Chibbar RN: Construction and characterization of a BAC library of a cold-tolerant hexaploid wheat cultivar. Crop Sci 45:1574–1577 (2005).
54.
Röder M, Hanemann A, Šimková H, Doležel J: Genetic dissection of a QTL for grain size in wheat, in: Abstracts of the 19th International Triticeae Mapping Initiative – 3rd COST Tritigen, p 43, INRA, Clermont-Ferrand (2009).
55.
Šafář J, Bartoš J, Janda J, Bellec A, Kubaláková M, et al: Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat. Plant J 39:960–968 (2004).
56.
Šafář J, Šimková H, Kubaláková M, Suchánková P, Číhálíková J: Generating resources for genomics of wheat homoeologous chromosome group 3: 3AS- and 3DS-specific BAC libraries. J Genet Breeding 61:151–160 (2007).
57.
Saintenac C, Falque M, Martin OC, Paux E, Feuillet C, et al: Detailed recombination studies along chromosome 3B provide new insights on crossover distribution in wheat (Triticum aestivum L.). Genetics 181:393–403 (2009).
58.
Sears ER: The aneuploids of common wheat. Missouri Agric Exp Stn Res Bull 572:1–58 (1954).
59.
Sears ER, Sears LMS: The telocentric chromosomes of common wheat, in Ramanujam S (ed): Proceedings of the 5th International Wheat Genetics Symposium, pp 389–407, Indian Society of Genetics and Plant Breeding, New Delhi (1978).
60.
Sehgal SK, Li W, Rabinowicz P, Luo MC, Choulet F, et al: Sequence based comparison of Mega-base homoeologous regions of A and B genomes of bread wheat, in: Book of Abstracts, 19th International Triticeae Mapping Initiative and 3rd COST Tritigen, p 63, INRA, Clermont-Ferrand (2009).
61.
Shen B, Wang DM, McIntyre CL, Liu CJ: A ‘Chinese Spring’ wheat (Triticum aestivum L.) bacterial artificial chromosome library and its use in the isolation of SSR markers for targeted genome regions. Theor Appl Genet 111:1489–1494 (2005).
62.
Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, et al: Cloning and stable maintenance of 300-kilobasepair fragment of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 89:8794–8797 (1992).
63.
Šimková H, Číhalíková J, Vrána J, Lysák MA, Doležel J: Preparation of HMW DNA from plant nuclei and chromosomes isolated from root tips. Biol Plant 46:369–373 (2003).
64.
Šimková H, Šafář J, Suchánková P, Kovář vá P, Bartoš J, et al: 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 (2008).
65.
Šimková H, Valárik M, Lapitan N, Peng J, Ma Y, et al: Towards positional cloning of a Russian wheat aphid resistance gene on chromosome 7D of wheat, in: Abstracts of the International Conference ‘Plant and Animal Genomes XVIII’, P 300 (Sherago International, Inc., San Diego 2010).
66.
Soderlund C, Humphrey S, Dunhum A, French L: Contigs built with fingerprints, markers and FPC V4.7. Genome Res 10:1772–1787 (2000).
67.
Somers DJ, Kirkpatrick R, Moniwa M, Walsh A: Mining single-nucleotide polymorphisms from hexaploid wheat ESTs. Genome 46:431–437 (2003).
68.
Spielmeyer W, Mago R, Šimková H, Doležel J, Paux E, et al: Molecular dissection of durable stem rust resistance gene locus in wheat, in: Abstracts of the International Conference ‘Plant and Animal Genomes XVII’, P W283 (Sherago International, Inc., San Diego 2009).
69.
Suenaga K, Khairallah M, William HM, Hoisington DA: A new intervarietal linkage map and its application for quantitative trait locus analysis of ‘gigas’ features in bread wheat. Genome 48:65–75 (2005).
70.
Tao Q, Chang YL, Wang J, Chen H, Islam-Faridi MN, et al: Bacterial artificial chromosome-based physical map of the rice genome constructed by restriction fingerprint analysis. Genetics 158:1711–1724 (2001).
71.
van Schriek M, Feron R, van Oeveren J, de Heer P, DaPonte L, et al: Whole genome profiling of Solanum lycopersicum Heinz 1706, in: Abstracts of the 6th Solanaceae Genome Workshop 2009, p 297, New Delhi, India (2009).
72.
Vrána J, Kubaláková M, Šimková H, Číhalíková J, Lysák MA, Doležel J: Flow-sorting of mitotic chromosomes in common wheat (Triticum aestivum L.). Genetics 156:2033–2041 (2000).
73.
Wicker T, Yahiaoui N, Guyot R, Schlagenhauf E, Liu ZD, et al: Rapid genome divergence at orthologous low molecular weight glutenin loci of the A and Am genomes of wheat. Plant Cell 15:1186–1197 (2003).
74.
Wicker T, Schlagenhauf E, Graner A, Close TJ, Keller B, Stein N: 454 sequencing put to the test using the complex genome of barely. BMC Genomics 7:275 (2006).
75.
Wollenweber B, Porter JR, Lubberstedt T: Need for multidisciplinary research towards a second green revolution. Curr Opin Plant Biol 8:337–341 (2005).
76.
Yahiaoui N, Srichumpa P, Dudler R, Keller B: Genome analysis at different ploidy levels allows cloning of the powdery mildew resistance gene Pm3b from hexaploid wheat. Plant J 37:528–538 (2004).
77.
Zhang HB, Woo SS, Wing RA: BAC, YAC and cosmid library construction, in Foster GD, Twell D (eds): Plant Gene Isolation: Principles and Practice, pp 75–99 (John Wiley, New York 1996).
78.
Zhang HB, Wu C: BAC as tools for genome sequencing. Plant Physiol Biochem 39:195–209 (2001).
79.
Zhang P, Li W, Fellers J, Friebe B, Gill BS: BAC-FISH in wheat identifies chromosome landmarks consisting of different types of transposable elements. Chromosoma 112:288–299 (2004).
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