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Comparative sequence and genetic analyses of asparagus BACs reveal no microsynteny with onion or rice

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Abstract

The Poales (includes the grasses) and Asparagales [includes onion (Allium cepa L.) and asparagus (Asparagus officinalis L.)] are the two most economically important monocot orders. The Poales are a member of the commelinoid monocots, a group of orders sister to the Asparagales. Comparative genomic analyses have revealed a high degree of synteny among the grasses; however, it is not known if this synteny extends to other major monocot groups such as the Asparagales. Although we previously reported no evidence for synteny at the recombinational level between onion and rice, microsynteny may exist across shorter genomic regions in the grasses and Asparagales. We sequenced nine asparagus BACs to reveal physically linked genic-like sequences and determined their most similar positions in the onion and rice genomes. Four of the asparagus BACs were selected using molecular markers tightly linked to the sex-determining M locus on chromosome 5 of asparagus. These BACs possessed only two putative coding regions and had long tracts of degenerated retroviral elements and transposons. Five asparagus BACs were selected after hybridization of three onion cDNAs that mapped to three different onion chromosomes. Genic-like sequences that were physically linked on the cDNA-selected BACs or genetically linked on the M-linked BACs showed significant similarities (e < −20) to expressed sequences on different rice chromosomes, revealing no evidence for microsynteny between asparagus and rice across these regions. Genic-like sequences that were linked in asparagus were used to identify highly similar (e < −20) expressed sequence tags (ESTs) of onion. These onion ESTs mapped to different onion chromosomes and no relationship was observed between physical or genetic linkages in asparagus and genetic linkages in onion. These results further indicate that synteny among grass genomes does not extend to a sister order in the monocots and that asparagus may not be an appropriate smaller genome model for plants in the Asparagales with enormous nuclear genomes.

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Acknowledgments

This work was completed in compliance with the current laws governing genetic experimentation in the United States and was supported by the Initiative for Future Agriculture and Food Systems Grant 2001-52100-11344 from the USDA Cooperative State Research, Education, and Extension Service; German Research Foundation DFG grant Ju 205/2-3; a Fulbright-Hayes Post-doctoral Fellowship to JJ; and a Boyscast Fellowship to AK.

Disclaimer: Names are necessary to report factually on available data; however, the US Department of Agriculture (USDA) neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable.

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Authors and Affiliations

  1. Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA

    Jernej Jakše, Anil Khar & Sergio Melgar

  2. Agronomy Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, 1000, Slovenia

    Jernej Jakše

  3. Plant Breeding Institute, Christian-Albrechts-University of Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany

    Alexa Telgmann & Christian Jung

  4. The Institute for Genomic Research, 9712 Medical Center Dr., Rockville, MD, 20850, USA

    Foo Cheung & Christopher D. Town

  5. Agricultural Research Service, USDA, Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA

    Michael J. Havey

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  1. Jernej Jakše
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Correspondence to Michael J. Havey.

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Communicated by J. S. Heslop-Harrison.

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Jakše, J., Telgmann, A., Jung, C. et al. Comparative sequence and genetic analyses of asparagus BACs reveal no microsynteny with onion or rice. Theor Appl Genet 114, 31–39 (2006). https://doi.org/10.1007/s00122-006-0407-y

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  • DOI: https://doi.org/10.1007/s00122-006-0407-y

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