Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses

John E. Bowers, Miguel A. Arias, Rochelle Asher, Jennifer A. Avise, Robert T. Ball, Gene A. Brewer, Ryan W. Buss, Amy H. Chen, Thomas M. Edwards, James C. Estill, Heather E. Exum, Valorie H. Goff, Kristen L. Herrick, Cassie L.James Steele, Santhosh Karunakaran, Gmerice K. Lafayette, Cornelia Lemke, Barry S. Marler, Shelley L. Masters, Joana M. McMillanLisa K. Nelson, Graham A. Newsome, Chike C. Nwakanma, Rosana N. Odeh, Cynthia A. Phelps, Elizabeth A. Rarick, Carl J. Rogers, Sean P. Ryan, Keimun A. Slaughter, Carol A. Soderlund, Haibao Tang, Rod A. Wing, Andrew H. Paterson

Research output: Contribution to journalArticle

116 Scopus citations

Abstract

Nearly finished sequences for model organisms provide a foundation from which to explore genomic diversity among other taxonomic groups. We explore genome-wide microsynteny patterns between the rice sequence and two sorghum physical maps that integrate genetic markers, bacterial artificial chromosome (BAC) fingerprints, and BAC hybridization data. The sorghum maps largely tile a genomic component containing 41% of BACs but 80% of single-copy genes that shows conserved microsynteny with rice and partially tile a nonsyntenic component containing 46% of BACs but only 13% of single-copy genes. The remaining BACs are centromeric (4%) or unassigned (8%). The two genomic components correspond to cytologically discernible "euchromatin" and "heterochromatin. " Gene and repetitive DNA distributions support this classification. Greater microcolinearity in recombinogenic (euchromatic) than nonrecombinogenic (heterochromatic) regions is consistent with the hypothesis that genomic rearrangements are usually deleterious, thus more likely to persist in nonrecombinogenic regions by virtue of Muller's ratchet. Interchromosomal centromeric rearrangements may have fostered diploidization of a polyploid cereal progenitor. Model plant sequences better guide studies of related genomes in recombinogenic than nonrecombinogenic regions. Bridging of 35 physical gaps in the rice sequence by sorghum BAC contigs illustrates reciprocal benefits of comparative approaches that extend at least across the cereals and perhaps beyond.

Original languageEnglish (US)
Pages (from-to)13206-13211
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume102
Issue number37
DOIs
StatePublished - Sep 13 2005
Externally publishedYes

Keywords

  • Comparative genomics
  • Oryza
  • Synteny

ASJC Scopus subject areas

  • General

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    Bowers, J. E., Arias, M. A., Asher, R., Avise, J. A., Ball, R. T., Brewer, G. A., Buss, R. W., Chen, A. H., Edwards, T. M., Estill, J. C., Exum, H. E., Goff, V. H., Herrick, K. L., Steele, C. L. J., Karunakaran, S., Lafayette, G. K., Lemke, C., Marler, B. S., Masters, S. L., ... Paterson, A. H. (2005). Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses. Proceedings of the National Academy of Sciences of the United States of America, 102(37), 13206-13211. https://doi.org/10.1073/pnas.0502365102