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Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana

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Abstract.

A growing body of research indicates that microsynteny is common among dicot genomes. However, most studies focus on just one or a few genomic regions, so the extent of microsynteny across entire genomes remains poorly characterized. To estimate the level of microsynteny between Medicago truncatula (Mt) and Glycine max (soybean), and also among homoeologous segments of soybean, we used a hybridization strategy involving bacterial artificial chromosome (BAC) contigs. A Mt BAC library consisting of 30,720 clones was screened with a total of 187 soybean BAC subclones and restriction fragment length polymorphism (RFLP) probes. These probes came from 50 soybean contig groups, defined as one or more related BAC contigs anchored by the same low-copy probe. In addition, 92 whole soybean BAC clones were hybridized to filters of HindIII-digested Mt BAC DNA to identify additional cases of cross-hybridization after removal of those soybean BACs found to be repetitive in Mt. Microsynteny was inferred when at least two low-copy probes from a single soybean contig hybridized to the same Mt BAC or when a soybean BAC clone hybridized to three or more low-copy fragments from a single Mt BAC. Of the 50 soybean contig groups examined, 54% showed microsynteny to Mt. The degree of conservation among 37 groups of soybean contigs was also investigated. The results indicated substantial conservation among soybean contigs in the same group, with 86.5% of the groups showing at least some level of microsynteny. One contig group was examined in detail by a combination of physical mapping and comparative sequencing of homoeologous segments. A TBLASTX similarity search was performed between 1,085 soybean sequences on the 50 BAC contig groups and the entire Arabidopsis genome. Based on a criterion of sequence homologues <100 kb apart, each with an expected value of ≤1e-07, seven of the 50 soybean contig groups (14%) exhibited microsynteny with Arabidopsis.

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Fig. 1A–D.
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Fig. 3A, B.

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Acknowledgements.

We thank S. Cannon, R. Denny, D. Danesh, D. Foster-Hartnett, K. Larson and L. Marek for helpful discussions and for providing valuable materials. We also thank R. Staggs and T. Schmidt for assistance with some computational analysis. This research was supported by National Science Foundation grants DBI 98-72664 and DBI 98-72565. This paper is published as part of the series of the Minnesota Agricultural Experiment Station.

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Authors and Affiliations

  1. Department of Plant Pathology, 495 Borlaug Hall, 1991 Upper Buford Circle, University of Minnesota, St. Paul, MN 55108, USA

    H. H. Yan, J. Mudge, D. Larsen & N. D. Young

  2. Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, 55108, USA

    N. D. Young

  3. Department of Plant Pathology, University of California, Davis, California, 95616, USA

    D.-J. Kim & D. R. Cook

  4. Department of Agronomy and USDA-ARS-Corn Insect and Crop Genetics Research Unit, Iowa State University, Ames, Iowa, 50011, USA

    R. C. Shoemaker

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  1. H. H. Yan
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  2. J. Mudge
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  3. D.-J. Kim
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  4. D. Larsen
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  5. R. C. Shoemaker
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  6. D. R. Cook
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  7. N. D. Young
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Correspondence to N. D. Young.

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Communicated by J. Dvorak

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Yan, H.H., Mudge, J., Kim, DJ. et al. Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana . Theor Appl Genet 106, 1256–1265 (2003). https://doi.org/10.1007/s00122-002-1183-y

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  • DOI: https://doi.org/10.1007/s00122-002-1183-y

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