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 Wing, Robin Buell

Research output: Contribution to journalArticle

30 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)3636-3641
Number of pages6
JournalNucleic acids research
Volume28
Issue number18
StatePublished - Sep 15 2000
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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  • Cite this

    Yuan, Q., Liang, F., Hsiao, J., Zismann, V., Benito, M. I., Quackenbush, J., Wing, R., & Buell, R. (2000). Anchoring of rice BAC clones to the rice genetic map in silico. Nucleic acids research, 28(18), 3636-3641.