Theoretical and Applied Genetics

, Volume 111, Issue 8, pp 1489–1494 | Cite as

A ‘Chinese Spring’ wheat (Triticum aestivum L.) bacterial artificial chromosome library and its use in the isolation of SSR markers for targeted genome regions

Original Paper

Abstract

A bacterial artificial chromosome (BAC) library was constructed from the bread wheat (Triticum aestivum L.) genotype ‘Chinese Spring’ (‘CS’). The library consists of 395,136 clones with an estimated average insert size of 157 kb. This library provides an estimated 3.4-fold genome coverage for this hexaploid species. The genome coverage was confirmed by RFLP analysis of single-copy RFLP clones. The CS BAC library was used to develop simple sequence repeat (SSR) markers for targeted genome regions using five sequence-tagged-site (STS) markers designed from the chromosome arm of 3BS. The SSR markers for the targeted genome region were successfully obtained. However, similar numbers of new SSR markers were also generated for the other two homoeologous group 3 chromosomes. This data suggests that BAC clones belonging to all three chromosomes of homoeologous group 3 were isolated using the five STS primers. The potential impacts of these results on marker isolation in wheat and on library screening in general are discussed.

References

  1. Allouis S, Moore G, Bellec A, Sharp R, Faivre Rampant P, Mortimer K, Pateyron S, Foote TN, Griffiths S, Caboche M, Chalhoub B (2003) Construction and characterization of a hexaploid wheat (Triticum aestivum L.) BAC library from the reference germplasm ‘Chinese Spring’. Cereal Res Commun 31:331–338Google Scholar
  2. Bennett MD, Leitch IJ (1995) Nuclear DNA amounts in Angiosperms. Ann Bot 76:113–176CrossRefGoogle Scholar
  3. Bhattamakki D, Dong J, Chhabra AK, Hart GE (2000) An integrated SSR and RFLP linkage map of Sorghum bicolor (L.) Moench. Genome 43:988–1002CrossRefPubMedGoogle Scholar
  4. Cenci A, Chantret N, Kong X, Gu Y, Anderson OD, Fahima T, Distelfeld A, Dubcovsky J (2003) Construction and characterization of a half million clone BAC library of durum wheat (Triticum turgidum ssp. durum). Theor Appl Genet 107:931–999CrossRefPubMedGoogle Scholar
  5. Chao S, Sharp PJ, Worland AJ, Warham EJ, Koebner RMD, Gale MD (1989) RFLP-based genetic maps of wheat homoeologous group 7 chromosomes. Theor Appl Genet 78:495–504CrossRefGoogle Scholar
  6. Cregan PB, Bhagwat AA, Akkaya MS, Rongwen J (1994) Microsatellite fingerprinting and mapping of soybean. Methods Mol Cell Biol 5:49–61Google Scholar
  7. Cregan PB, Mudge J, Fickus EW, Marek LF, Danesh D, Denny R, Shoemaker RC, Matthews BF, Jarvik T, Young ND (1999) Targeted isolation of simple sequence repeat markers through the use of bacterial artificial chromosomes. Theor Appl Genet 98:919–928CrossRefGoogle Scholar
  8. Devos KM, Bryan GJ, Collins AJ, Stephenson P, Gale MD (1995) Application of two microsatellite sequences in wheat storage proteins as molecular markers. Theor Appl Genet 90:247–252CrossRefGoogle Scholar
  9. Dubcovsky J, Ramakrishna W, SanMiguel PJ, Busso CS, Yan L, Shiloff BA, Bennetzen JL (2001) Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes. Plant Physiol 125:1342–1353CrossRefPubMedGoogle Scholar
  10. Endo TR, Gill BS (1996) The deletion stocks of common wheat. J Hered 87:295–307Google Scholar
  11. Faris JD, Fellers JP, Brooks SA, Gill BS (2003) A bacterial artificial chromosome contig spanning the major domestication locus Q in wheat and identification of a candidate gene. Genetics 164:311–321PubMedGoogle Scholar
  12. Gale MD, Miller TE (1988) The introduction of alien genetic variation into wheat. In: Lupton FGH (ed) Wheat breeding: its scientific basis, pp 173–210Google Scholar
  13. Gao LF, Tang JF, Li HW, Jia JZ (2003) Analysis of microsatellites in major crops assessed by computational and experimental approaches. Mol Breed 12:245–261CrossRefGoogle Scholar
  14. Humphry ME, Konduru V, Lambridges CJ, Magner T, McIntyre CL, Aitken EAB, Liu CJ (2002) Development of a mungbean (Vigna radiata) RFLP linkage map and its comparision with lablab (Lablab purpureus) reveals a high level of synteny between the two genomes. Theor Appl Genet 105:160–166CrossRefPubMedGoogle Scholar
  15. Janda J, Bartoš J, Šafář J, Kubaláková M, Valárik M, Číhalíková J, Šimková H, Caboche M, Sourdille P, Bernard M, Chaahoub B, Doležel J (2004) Construction of a subgenomic BAC library specific for chromosomes 1D, 4D and 6D of hexaploid wheat. Theor Appl Genet 109:1337–1345CrossRefPubMedGoogle Scholar
  16. Law CN, Snape JW, Worland AJ (1988) Aneuploidy in wheat and its uses in genetic analysis. In: Lupton FGH (ed) Wheat breeding: its scientific basis, pp 71–108Google Scholar
  17. Lijavetzhy D, Muzzi G, Wicker T, Keller B, Wing R, Dubcovsky J (1999) Construction and characterization of a bacterial artificial chromosome (BAC) library for the A genome of wheat. Genome 42:1176–1182CrossRefPubMedGoogle Scholar
  18. Liu S, Anderson JA (2003) Targeted molecular mapping of a major wheat QTL for Fusarium head blight resistance using wheat ESTs and synteny with rice. Genome 46:817–823CrossRefPubMedGoogle Scholar
  19. Liu CJ, Musial JM (2001) The application of chloroplast DNA clones in identifying maternal donors for polyploidy species of Stylosanthes. Theor Appl Genet 102:73–77CrossRefGoogle Scholar
  20. Liu CJ, Atkinson MD, Chinoy CN, Devos KM, Gale MD (1992) Non-homoeologous translocations between group 4, 5 and 7 chromosomes within wheat and rye. Theor Appl Genet 83:305–312CrossRefGoogle Scholar
  21. Ma Z, Weining S, Sharp PJ, Liu CJ (2000) Non-gridded library: a new approach for BAC (bacterial artificial chromosome) exploitation in hexaploid wheat (Triticum aestivum). Nucleic Acids Res 28(24):e106Google Scholar
  22. Manly KF, Cudmore RH Jr, Meer JM (2001) Map Manager QTL, cross-platform software for genetic mapping. Mammal Genome 12:930–932CrossRefPubMedGoogle Scholar
  23. Miyagi M, Humphry ME, Ma ZY, Bateson M, Liu CJ (2004) Construction of bacterial artificial chromosome clones and their application in developing PCR-based markers closely linked to a major locus conditioning bruchid resistance in mungbean (Vigna radiata L. Wilczek). Theor Appl Genet 110:151–156CrossRefPubMedGoogle Scholar
  24. Moullet O, Zhang HB, Lagudah ES (1999) Construction and characterization of a large DNA insert library from the D genome of wheat. Theor Appl Genet 99:305–313CrossRefGoogle Scholar
  25. Mozo T, Dewar K, Dunn P, Ecker JR, Fischer S, Kloska S, Lehrach H, Marra M, Martienssen R, Meier Ewert S, Altmann T (1999) A complete BAC-based physical map of the Arabidopsis thaliana genome. Nat Genet 22:271–275CrossRefPubMedGoogle Scholar
  26. Nilmalgoda SD, Cloutier S, Walichnowski AZ (2003) 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 46:870–878CrossRefPubMedGoogle Scholar
  27. Ogihara Y, Mochida K, Kawaura K, Murai K, Seki M, Kamiya A, Shinozaki K, Carninci P, Hayashizaki Y, Shin-I T, Kohara Y, Yamazaki Y (2004) Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characteization by large-scale sequencing of expressed sequence tags. Genes Genet Syst 79:227–232CrossRefPubMedGoogle Scholar
  28. Rajesh PN, Coyne C, Meksem K, DerSharma K, Gupta V, Muehlbauer FJ (2004) Construction of a HindIII bacterial artificial chromosome library and its use in identification of clones associated with disease resistance in chickpea. Theor Appl Genet 108:663–669CrossRefPubMedGoogle Scholar
  29. Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier M-H, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023PubMedGoogle Scholar
  30. Sears ER (1954) The aneuploids of common wheat. Mont Agric Exp Stn Res Bull 572:1–58Google Scholar
  31. Sears ER (1966) Nullisomic-tetrasomic combinations in hexaploid wheat. In: Riley R, Lewis KR (eds) Chromosome manipulation and plant genetics. Oliver and Boy, London, pp 29–45Google Scholar
  32. Sorrells ME, Rota ML, Bermudez-Kandianis CE, Greene RA, Kantety R, Munkvold JD, Miftahudin, Mahmoud A, Ma X, Gustafson PJ, Qi LL, Echalier B, Gill BS, Matthews DE, Lazo GR, Chao S, Anderson OD, Edwards H, Linkiewicz AM, Dubcovsky J, Akhunov ED, Dvorak J, Zhang D, Nguyen HT, Peng J, Lapitan NV, Gonzalez-Hernandez JL, Anderson JA, Hossain K, Kalavacharla V, Kianian SF, Choi DW, Close TJ, Dilbirligi M, Gill KS, Steber C, Walker-Simmons MK, McGuire PE, Qualset CO (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13:1818–1827PubMedGoogle Scholar
  33. Šafář J, Bartoš J, Janda J, Bellec A, Kubaláková M, Valárik M, Pateyron S, Weiserová J, Tušková R, Číhalíková J, Vrána J, Šimková H, Faivre-Rampant P, Sourdille P, Caboche M, Bernard M, Doležel J, Chalhoub B (2004) Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat. Plant J 39:960–968CrossRefPubMedGoogle Scholar
  34. Wang Z, Weber JL, Zhang G, Tanksley SD (1994) Survey of plant short tandem DNA repeats. Theor Appl Genet 88:1–6Google Scholar
  35. Zhang HB, Choi S, Woo SS, Li Z, Wing RA (1996) Construction and characterization of two rice bacterial artificial chromosome libraries from the parents of a permanent recombinant inbred mapping population. Mol Breed 2:11–24CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  1. 1.CSIRO Plant IndustrySt LuciaAustralia
  2. 2.College of life scienceHebei Agricultural UniversityHebeiChina

Personalised recommendations