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Functional Analysis of the Gossypium arboreum Genome

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Abstract

Gossypium arboreum is an Old World relative of the more commonly cultivated commercial species Gossypium hirsutum, a newer genetic line formed in the New World. G. arboreum has the important property that it can be cultivated in severely hot, dry climates. The genome of G. arboreum has not been completely sequenced, and annotation for the genome is not extensive. We studied the genome of G. arboreum by using cross-species hybridization studies with genomic microarrays for the more annotated species, Arabidopsis thaliana and Oryza sativa. Approximately 30% of the probes on the A. thaliana and O. sativa microarrays were hybridized effectively by target samples prepared from G. arboreum genomic DNA. Many of genes tentatively identified by hybridization function in various levels of the stress response. Cross-species hybridization can provide effective clues as to potentially valuable genes that may be present in a less well-studied species such as G. arboreum. The stress response genes tentatively identified in these studies should provide useful clues for further studies toward the development of hardier strains of cotton.

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Acknowledgments

Uzma Quaisar was supported by a UNESCO Fellowship Program in Support of Priority Program Areas (2006–2007). We thank Georgina Lambert for her constructive comments in the preparation of this manuscript.

Authors’ contributions

Roger Barthelson helped develop the goals for this project, guided the laboratory work, performed much of the advanced annotational analysis, and did most of the writing for the manuscript. Uzma Qaisar performed all of the experimental work, helped develop the aims of the project, did most of the primary analysis, and wrote the results for the manuscript. David Galbraith provided laboratory space, funding for materials, including the microarrays, which were printed in his laboratory, and some training for Uzma Qaisar.

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Authors and Affiliations

  1. Department of Plant Sciences, Forbes 303, University of Arizona, Tucson, AZ, 85721, USA

    Roger A. Barthelson, Uzma Qaisar & David W. Galbraith

Authors
  1. Roger A. Barthelson
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  2. Uzma Qaisar
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  3. David W. Galbraith
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Correspondence to Roger A. Barthelson.

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Additional Table 1

A comparison of hybridization vs. homology with known Gossypium species sequences for some of the microarray probes on the Arabidopsis and Oryza microarrays (XLS 17 kb)

Supplemental Figure 1

Mapping of G. arboreum homologs on the G. hirsutum genome. The sequences for Arabidopsis microarray oligonucleotides that were significantly hybridized by the G. arboreum genomic DNA were used for BLAST analysis against the G. hirsutum genome. Here, the number of homologs found by BLAST is plotted for each chromosome. Refer to Rong et al. 2004 Genetics 166:389-417 (DOC 189 kb)

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Barthelson, R.A., Qaisar, U. & Galbraith, D.W. Functional Analysis of the Gossypium arboreum Genome. Plant Mol Biol Rep 28, 334–343 (2010). https://doi.org/10.1007/s11105-009-0157-5

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