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Nucleic Acids Research, 2000, Vol. 28, No. 18 3636-3641
© 2000 Oxford University Press

Anchoring of rice BAC clones to the rice genetic map in silico

Qiaoping Yuan, Feng Liang, Joseph Hsiao, Victoria Zismann, Maria-Ines Benito, John Quackenbush, Rod Wing1 and Robin Buell*

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA and 1Clemson University Genomics Institute, 100 Jordan Hall, Clemson, SC 29634-5708, USA

A wealth of molecular resources have been developed for rice genomics, including dense genetic maps, expressed sequence tags (ESTs), yeast artificial chromosome maps, bacterial artificial chromosome (BAC) libraries and BAC end sequence databases. Integration of genetic and physical maps involves labor-intensive empirical experiments. To accelerate the integration of the bacterial clone resources with the genetic map for the International Rice Genome Sequencing Project, we cleaned and filtered the available EST and BAC end sequences for repetitive sequences and then searched all available rice genetic markers with our filtered databases. We identified 418 genetic markers that aligned with at least one BAC end sequence with >95% sequence identity, providing a set of large insert clones with an average separation of 1 Mb that can serve as nucleation points for the sequencing phase of the International Rice Genome Sequencing Project.

* To whom correspondence should be addressed. Tel: +1 301 838 3558; Fax: +1 301 838 0208; Email: rbuell@tigr.org


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