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Leveraging the rice genome sequence for monocot comparative and translational genomics

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Abstract

Common genome anchor points across many taxa greatly facilitate translational and comparative genomics and will improve our understanding of the Tree of Life. To add to the repertoire of genomic tools applicable to the study of monocotyledonous plants in general, we aligned Allium and Musa ESTs to Oryza BAC sequences and identified candidate Allium-Oryza and Musa-Oryza conserved intron-scanning primers (CISPs). A random sampling of 96 CISP primer pairs, representing loci from 11 of the 12 chromosomes in rice, were tested on seven members of the order Poales and on representatives of the Arecales, Asparagales, and Zingiberales monocot orders. The single-copy amplification success rates of Allium (31.3%), Cynodon (31.4%), Hordeum (30.2%), Musa (37.5%), Oryza (61.5%), Pennisetum (33.3%), Sorghum (47.9%), Zea (33.3%), Triticum (30.2%), and representatives of the palm family (32.3%) suggest that subsets of these primers will provide DNA markers suitable for comparative and translational genomics in orphan crops, as well as for applications in conservation biology, ecology, invasion biology, population biology, systematic biology, and related fields.

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Acknowledgments

This work was supported by grants from the Rockefeller Foundation and USAID- CCGI to AHP, FAF, and HS; and NSF EF−0542228 to CDB as well as the Biotechnology Overseas Associateship of the Department of Biotechnology, Ministry of Science & Technology, Government of India to HCL.

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Authors and Affiliations

  1. Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA

    H. C. Lohithaswa, F. A. Feltus, H. P. Singh & A. H. Paterson

  2. University of Agricultural Sciences, Krishinagar, Dharwad, 580005, India

    H. C. Lohithaswa

  3. N.D. University of Agriculture and Technology, Kumarganj, Faizabad, 224264, Uttar Pradesh, India

    H. P. Singh

  4. Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA

    C. D. Bacon & C. D. Bailey

Authors
  1. H. C. Lohithaswa
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  2. F. A. Feltus
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  3. H. P. Singh
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  4. C. D. Bacon
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  5. C. D. Bailey
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  6. A. H. Paterson
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Corresponding author

Correspondence to A. H. Paterson.

Additional information

Communicated by E. Guiderdoni.

H. C. Lohithaswa and F. A. Feltus contributed equally to this work.

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Lohithaswa, H.C., Feltus, F.A., Singh, H.P. et al. Leveraging the rice genome sequence for monocot comparative and translational genomics. Theor Appl Genet 115, 237–243 (2007). https://doi.org/10.1007/s00122-007-0559-4

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  • DOI: https://doi.org/10.1007/s00122-007-0559-4

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