Poster: Genomics Resources
Abs #
948: The barley microarray
A microarray chip representing approximately 22,000 barley unigenes has been produced as part of a USDA-IFAFS project entitled, “An integrated physical and expression map of barley for Triticeae improvement”. The content of the chip was derived from more than 400,000 barley EST sequences received from cooperators in USA, Germany, Japan, Scotland, and Finland, plus about 1,000 sequences retrieved from the GenBank nr database by Roger Wise and co-workers at Iowa State University. All EST sequences were trimmed to high quality regions, contaminants were identified and removed, and the remaining information was compiled using the CAP3 algorithm. A “stringent” assembly (paralogs separated) contained a total of about 53,000 “unigenes” (the sum of contigs plus singletons), among which about 50% had reliable 3’ ends. From these sequences with reliable 3’ ends the microarray chip content was defined. Probe sets were then designed and the chip fabricated by Affymetrix. The availability of this barley microarray has made it possible to examine barley gene expression on a large scale. Processes that are important to abiotic stress adaptation, disease resistance, and seed quality are now being studied using this new analytical tool. Details on the content of the barley microarray can be viewed using the free public software HarvEST:Triticeae, which is available as a Windows installation file from http://harvest.ucr.edu.
