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Published on January 13, 2006; 10.1104/pp.105.073809

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Received November 4, 2005
Returned for revision December 12, 2005
Accepted January 4, 2006

A segment of the Apospory Specific Genomic Region (ASGR) is highly microsyntenic not only between the apomicts Pennisetum squamulatum and Cenchrus ciliaris, but also with a rice chromosome 11 centromeric-proximal genomic region

Gustavo Gualtieri , Joann A. Conner , Daryl T. Morishige , L. David Moore , John E. Mullet , and Peggy Ozias-Akins *

Department of Horticulture, The University of Georgia Tifton Campus, Tifton, GA 31793-0748; Present address: School of Integrative Biology, Faculty of Biological and Chemical Sciences, The University of Queensland, Brisbane Qld 4072 Australia
Department of Horticulture, The University of Georgia Tifton Campus, Tifton, GA 31793-0748
Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843

* Corresponding author; email: pozias{at}uga.edu.

Bacterial artificial chromosome (BAC) clones from the apomicts, Pennisetum squamulatum and Cenchrus ciliaris (buffelgrass), isolated with the apospory-specific genomic region (ASGR)-marker ugt197, were assembled into contigs that were extended by chromosome walking. Gene-like sequences from contigs were identified by shotgun sequencing and BLAST searches, and used to isolate orthologous rice contigs. Additional gene-like sequences in the apomicts' contigs were identified by bioinformatics using fully sequenced BACs from orthologous rice contigs as templates, as well as by inter-species, whole-contig cross-hybridizations. Hierarchical contig orthology was rapidly assessed by constructing detailed long-range contig molecular maps showing the distribution of gene-like sequences and markers, and searching for microsyntenic patterns of sequence identity and spatial distribution within and across species contigs. We found microsynteny between P. squamulatum and C. ciliaris contigs. Importantly, this approach also enabled us to isolate from within the rice (Oryza sativa L.) genome, contig RA, which shows the highest microsynteny and is most orthologous to the ugt197-containing C1C buffelgrass contig. Contig RA belongs to the rice genome database contig 77 (according to the current 12 September 2003 rice FPC build) that maps proximal to the chromosome 11 centromere, a feature that interestingly correlates with the mapping of ASGR-linked BACs proximal to the centromere or centromere-like sequences. Thus, relatedness between these two orthologous contigs is supported both by their molecular micro-structure and by their centromeric-proximal location. Our discoveries promote the use of a microsynteny-based positional cloning approach using the rice genome as a template to aid in constructing the ASGR towards the isolation of genes underlying apospory.




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