Molecular Breeding

, Volume 8, Issue 3, pp 255–261

Development of genomic resources for cotton (Gossypium hirsutum L.): BAC library construction, preliminary STC analysis, and identification of clones associated with fiber development

  • J.P. Tomkins
  • D.G. Peterson
  • T.J. Yang
  • D. Main
  • T.A. Wilkins
  • A.H. Paterson
  • R.A. Wing
Article

Abstract

We have constructed a cotton (Gossypium hirsutum L.) BAC library using the elite Acala-type cultivar Maxxa. The BAC library contains 129 024 clones comprising 8.3 haploid genome equivalents based on a AD genome size of 2118 Mb. A random sampling of 435 BACs indicated an average insert length of 137 kb with a range of 80 to 275 kb, and 1.4% of the BACs do not contain inserts. Of the BAC clones in the sample 99% had an average insert length equal to or greater than 100 kb. Contamination of the genomic library with chloroplast clones was low (1.5%). To evaluate the library for genome representation and to identify clones associated with cotton fiber development, six BAC colony filters (7.2× representation) were screened with PCR-generated gene-specific probes for the GhMYB class of transcription factor genes giving an average of 12 positive signals per probe (range 6–20). To gain a glimpse into the cotton genome and evaluate the library for sequence-tagged connector (STC) development, 1536 BAC clones were end sequenced in both forward and reverse direction. The STCs were queried against the SwissProt and MIPS Arabidopsis databases and significant hits were sorted according to putative function.

Cotton BAC library BAC end sequencing GhMYB genes 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Arumuganathan K. and Earle E. 1991. Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9: 208–218.Google Scholar
  2. 2.
    Bairoch A. and Apweiler R. 2000. The SWISS-PROT protein sequence database and its supplement TrEMBL Nucl. Acids Res. 28: 45–48.Google Scholar
  3. 3.
    Beasely J. 1942. Meiotic chromosome behaviour in species hybrids, haploids, and induced polyploids of Gossypium. Genetics 27: 25–54.Google Scholar
  4. 4.
    Budiman A., Mao L., Wood T. and Wing R. 2000. A deepcoverage tomato BAC library and prospects toward development of an STC framework for genome sequencing. Genome Res. 10: 129–136.Google Scholar
  5. 5.
    Brubaker C., Paterson A., and Wendel J. 1999. Comparative genetic mapping of allotetraploid cotton and its diploid progenitors. Genome 42: 184–203.Google Scholar
  6. 6.
    Carina D., and Surridge C. 2000. A. thaliana genome. Nature 408: 791.Google Scholar
  7. 7.
    Endrizzi J., Turcotte E. and Kohel R. 1985. Genetics, cytology, and evolution of Gossypium. Adv. Genet. 23: 271–375.Google Scholar
  8. 8.
    Ewing B. and Green P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186–194.Google Scholar
  9. 9.
    Ewing B., Hillier L., Wendl M. and Green P. 1998. Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8: 175–185.Google Scholar
  10. 10.
    Fryxell P. 1992. A revised taxonomic interpretation of Gossypium L. (Malvaceae). Rheedea 2: 108–165.Google Scholar
  11. 11.
    Loguercio L., Zhang J. and Wilkins T. 2000. Six novel myb genes are spatially and temporally regulated during expansion of developing cotton trichomes in two distinct expression patterns. Plant J. (in press)Google Scholar
  12. 12.
    Luo M., Wang Y., Frisch D., Joobeur T., Wing R and Dean R. 2001. Melon BAC library construction using improved methods and identification of clones linked to the locus conferring resistance tomelon Fusarium wilt (Fom-2). Genome (in press).Google Scholar
  13. 13.
    Mewes H., Heumann K., Kaps A., Mayer K., Pfeiffer F., Stocker S. and Frishman D. 1999. MIPS: a database for genomes and protein sequences. Nucl. Acids Res. 27: 44–48Google Scholar
  14. 14.
    Peterson D., Tomkins J., Frisch D., Wing R. and Paterson A. 2000. Construction of plant bacterial artificial chromosome (BAC) libraries: an illustrated guide. J. Agric. Genomics vol. 5 (http://www.ncgr.org).Google Scholar
  15. 15.
    Reinisch A., Dong J., Brubaker D., Stelly D., Wendel J. and Paterson A. 1994. A detailed RFLP map of cotton (Gossypium hirsutuum × G. barbadense): chromosome organization and evolution in a disomic polyploid genome. Genetics 138: 829–847.Google Scholar
  16. 16.
    Sambrook J., Frisch E. and Maniatis T. 1989. Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory Press, Plainview, NY.Google Scholar
  17. 17.
    Shizuya H., Birren B., Kim U., Mancino V., Slepak T., Tachiiri Y. and Simon M. 1992. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc. Natl. Acad. Sci USA 89: 8794–8797.Google Scholar
  18. 18.
    Tomkins J.P., Mahalingham R., Miller-Smith H., Goicoechea J.L., Knapp H.T. and Wing R.A. 1999a. A soybean bacterial artificial chromosome library for PI 437654 and the identification of clones associated with cyst nematode resistance. Plant Mol. Biol. 41: 25–32. 261Google Scholar
  19. 19.
    Tomkins J., Yu Y., Miller-Smith H., Frisch D., Woo S. and Wing R. 1999b. A bacterial artificial chromosome library for sugarcane. Theor. Appl. Genet. 99: 419–424.Google Scholar
  20. 20.
    Venter C., Smith H. and Hood L. 1996. A new strategy for genome sequencing. Science 381: 364–366.Google Scholar
  21. 21.
    Woo S., Jiang J., Gill B., Paterson A. and Wing R. 1994. Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. Nucl. Acids Res. 22: 4922–4931.Google Scholar
  22. 22.
    Yu Y., Tomkins J., Waugh R., Frisch D., Kudrna D., Kleinhofs A., Brueggeman R., Muehlbauer G., Wise R. and Wing R. 2000. A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes. Theor. Appl. Gen. 101: 1093–1099.Google Scholar

Copyright information

© Kluwer Academic Publishers 2001

Authors and Affiliations

  • J.P. Tomkins
    • 1
  • D.G. Peterson
    • 2
  • T.J. Yang
    • 1
  • D. Main
    • 1
  • T.A. Wilkins
    • 3
  • A.H. Paterson
    • 4
  • R.A. Wing
    • 1
  1. 1.Clemson University Genomics Institute, Room 100, Jordan HallClemsonUSA
  2. 2.Department of BotanyUniversity of GeorgiaAthensUSA
  3. 3.Department of Agronomy and Range ScienceUniversity of CaliforniaDavisUSA
  4. 4.Center for Applied Genetic TechnologyUniversity of GeorgiaAthensUSA

Personalised recommendations