ARS | Publication request: COMPARATIVE BIOINFORMATIC ANALYSIS OF GENETIC MAPS FROM RICE AND MAIZE

Submitted to: Maize Genetics Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: March 14, 2002
Publication Date: March 14, 2002
Citation: FANG, Z., POLACCO, M.L., COE JR, E.H. COMPARATIVE BIOINFORMATIC ANALYSIS OF GENETIC MAPS FROM RICE AND MAIZE. MAIZE GENETICS CONFERENCE ABSTRACTS. 2002. p. 38.

Technical Abstract: Comparative genomics research facilitates the identification and manipulation of agronomically important genes and traits among crops by utilizing information from various genome databases, sequence depositories, and other information systems. For the integration and comparison of information, bioinformatics provides and uses the tools to analyze and visualize these genomic data. In collaboration with the Japanese Rice Genome Research Program (RGP), we have developed software, cMap, a tool for graphical genome mapping comparison with text lists of shared locus information within or across species. By using cMap, genomic information from various maize genetic maps and the rice RGP2000 map has been compared and analyzed. Intra-genomic comparisons reveal duplicated regions in the maize genome. Comparing several maize maps where different SSRs have been resolved facilitates marker selection, as there are only 0.4% of SSRs among SSR maps that have two or more loci, whereas other maps, such as UMC98 and BNL96, have at least 20% of markers that hit two or more loci. Therefore, SSR can be used as a specific marker for the identification and manipulation of genes and traits in comparative genomic research. Inter-genomic comparisons between the rice RGP2000 map and maize UMC98 or Pioneer90 composite map confirm that maize has more duplicated regions of the genome than rice and shows that syntenic relationships are revealed in some regions of the chromosomes between rice and maize, and need more underlying probe data in support. The cMap is accessible at http://www.agron.missouri.edu/cMapDB/cMap.html. Supported by NSF Plant Genome Grant DBI 9872655.